System OS: Linux, Architecture: amd64 Java Info: 11.0.23, OpenJDK 64-Bit Server VM, Ubuntu .NET Core Info: N/A Version info: FragPipe version 21.1 MSFragger version 4.0 IonQuant version 1.10.12 Philosopher version 5.1.0 LCMS files: Experiment/Group: CatA_0000_1 (if "spectral library generation" is enabled, all files will be analyzed together) - /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0000_1.raw DDA Experiment/Group: CatA_0000_2 (if "spectral library generation" is enabled, all files will be analyzed together) - /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0000_2.raw DDA Experiment/Group: CatA_0000_3 (if "spectral library generation" is enabled, all files will be analyzed together) - /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0000_3.raw DDA Experiment/Group: CatA_0000_4 (if "spectral library generation" is enabled, all files will be analyzed together) - /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0000_4.raw DDA Experiment/Group: CatA_0030_1 (if "spectral library generation" is enabled, all files will be analyzed together) - /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0030_1.raw DDA Experiment/Group: CatA_0030_2 (if "spectral library generation" is enabled, all files will be analyzed together) - /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0030_2.raw DDA Experiment/Group: CatA_0030_3 (if "spectral library generation" is enabled, all files will be analyzed together) - /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0030_3.raw DDA Experiment/Group: CatA_0030_4 (if "spectral library generation" is enabled, all files will be analyzed together) - /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0030_4.raw DDA Experiment/Group: CatA_0090_1 (if "spectral library generation" is enabled, all files will be analyzed together) - /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0090_1.raw DDA Experiment/Group: CatA_0090_2 (if "spectral library generation" is enabled, all files will be analyzed together) - /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0090_2.raw DDA Experiment/Group: CatA_0090_3 (if "spectral library generation" is enabled, all files will be analyzed together) - /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0090_3.raw DDA Experiment/Group: CatA_0090_4 (if "spectral library generation" is enabled, all files will be analyzed together) - /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0090_4.raw DDA Experiment/Group: CatB_0000_1 (if "spectral library generation" is enabled, all files will be analyzed together) - /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0000_1.raw DDA Experiment/Group: CatB_0000_2 (if "spectral library generation" is enabled, all files will be analyzed together) - /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0000_2.raw DDA Experiment/Group: CatB_0000_3 (if "spectral library generation" is enabled, all files will be analyzed together) - /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0000_3.raw DDA Experiment/Group: CatB_0000_4 (if "spectral library generation" is enabled, all files will be analyzed together) - /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0000_4.raw DDA Experiment/Group: CatB_0015_1 (if "spectral library generation" is enabled, all files will be analyzed together) - /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0015_1.raw DDA Experiment/Group: CatB_0015_2 (if "spectral library generation" is enabled, all files will be analyzed together) - /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0015_2.raw DDA Experiment/Group: CatB_0015_3 (if "spectral library generation" is enabled, all files will be analyzed together) - /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0015_3.raw DDA Experiment/Group: CatB_0015_4 (if "spectral library generation" is enabled, all files will be analyzed together) - /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0015_4.raw DDA Experiment/Group: CatB_0060_1 (if "spectral library generation" is enabled, all files will be analyzed together) - /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0060_1.raw DDA Experiment/Group: CatB_0060_2 (if "spectral library generation" is enabled, all files will be analyzed together) - /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0060_2.raw DDA Experiment/Group: CatB_0060_3 (if "spectral library generation" is enabled, all files will be analyzed together) - /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0060_3.raw DDA Experiment/Group: CatB_0060_4 (if "spectral library generation" is enabled, all files will be analyzed together) - /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0060_4.raw DDA Experiment/Group: CatC_0000_1 (if "spectral library generation" is enabled, all files will be analyzed together) - /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0000_1.raw DDA Experiment/Group: CatC_0000_2 (if "spectral library generation" is enabled, all files will be analyzed together) - /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0000_2.raw DDA Experiment/Group: CatC_0000_3 (if "spectral library generation" is enabled, all files will be analyzed together) - /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0000_3.raw DDA Experiment/Group: CatC_0000_4 (if "spectral library generation" is enabled, all files will be analyzed together) - /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0000_4.raw DDA Experiment/Group: CatC_0030_1 (if "spectral library generation" is enabled, all files will be analyzed together) - /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0030_1.raw DDA Experiment/Group: CatC_0030_2 (if "spectral library generation" is enabled, all files will be analyzed together) - /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0030_2.raw DDA Experiment/Group: CatC_0030_3 (if "spectral library generation" is enabled, all files will be analyzed together) - /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0030_3.raw DDA Experiment/Group: CatC_0030_4 (if "spectral library generation" is enabled, all files will be analyzed together) - /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0030_4.raw DDA Experiment/Group: CatC_0090_1 (if "spectral library generation" is enabled, all files will be analyzed together) - /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0090_1.raw DDA Experiment/Group: CatC_0090_2 (if "spectral library generation" is enabled, all files will be analyzed together) - /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0090_2.raw DDA Experiment/Group: CatC_0090_3 (if "spectral library generation" is enabled, all files will be analyzed together) - /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0090_3.raw DDA Experiment/Group: CatC_0090_4 (if "spectral library generation" is enabled, all files will be analyzed together) - /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0090_4.raw DDA Experiment/Group: CatD_0000_1 (if "spectral library generation" is enabled, all files will be analyzed together) - /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0000_1.raw DDA Experiment/Group: CatD_0000_2 (if "spectral library generation" is enabled, all files will be analyzed together) - /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0000_2.raw DDA Experiment/Group: CatD_0015_1 (if "spectral library generation" is enabled, all files will be analyzed together) - /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0015_1.raw DDA Experiment/Group: CatD_0015_2 (if "spectral library generation" is enabled, all files will be analyzed together) - /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0015_2.raw DDA Experiment/Group: CatD_0015_3 (if "spectral library generation" is enabled, all files will be analyzed together) - /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0015_3.raw DDA Experiment/Group: CatD_0015_4 (if "spectral library generation" is enabled, all files will be analyzed together) - /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0015_4.raw DDA 471 commands to execute: CheckCentroid java -Xmx56G -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/tools/batmass-io-1.30.0.jar com.dmtavt.fragpipe.util.CheckCentroid /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0000_1.raw 23 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/ce4d5a4b-7c25-4981-8658-3a9ef82d46bd WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/5787929d-c2f8-4a5f-a975-86ec494f8f3c WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/99347bc6-617b-48b3-9430-7360063e3646 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/43fb631b-845b-4b97-9f86-d6b0aa80f423 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/5c52d430-2d67-467b-a881-4dcc93bd6d63 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/1da1a03b-1800-45d7-b50e-17e3ce7af667 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/fc6b848f-b734-4a53-bf8a-a4c312532ee7 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/1204c0bb-3cbe-445f-b42d-395578f716c4 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/b6793aed-7f17-4fc9-9935-faa36f11ce97 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/0e5d87de-a9ac-4747-8d3d-d42d4fdff3e3 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/87f586d6-7c14-4842-87d2-8c83edd7ae45 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/1b4f5fe5-16b0-48c8-a198-c6d0e85fc308 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/473986bb-96e0-440d-87d5-cc9e29c822d0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/9d05af0f-b5af-4572-af95-a9efad0dafe0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/d38f0150-a938-4177-9155-b9fc21f95a01 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/0c4ec3ac-186f-43b1-85e9-a98cdc3b40ea WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/455b595e-8ee9-4930-8e26-56c68a8585e0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/3c931408-69fe-401c-8dad-8493085b210d WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/38cdd109-15af-48bf-8c83-79370e97d897 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/fa351ef3-e932-42e9-89e7-d90b1959fa3a WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/9eb5deff-fe65-476d-8f8b-30ddc64e7676 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/4ec418cb-4f5e-43bb-86bb-f92cdfa9820b WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0000_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0000_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/e5b06af0-c0e1-433b-8678-4a1ab86f80bc WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0000_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0000_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/64b0412e-129c-4db1-86ec-c782657b76d4 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/041aa3fa-2317-4a5b-b08c-5e517c79ab8c WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/2185cb32-4c72-461d-8cf1-4b32b3a2a1f4 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/662ce773-19cf-4eb6-96d7-3cf5b553b345 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/10eba5ff-5dc3-407a-ade1-fdb03f52a678 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/bf613636-b982-47c5-84a8-2482f1efdbab WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/fcf7c3b0-d20f-43ef-b05c-d20493b794b0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/c41b1b55-aa88-4980-bb47-305e289b05d2 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/611c8b54-552a-431c-bd2b-f956e593b575 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/d9f9550b-7cfa-4203-874b-2ce8aa42cfb4 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/6f8326f7-69a9-40c8-ab37-2baa2656edfe WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/08409ab1-e96f-4aad-8052-9680f72e2a0a WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/70f75b0b-ad72-4518-9d96-3d0ff16508f8 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/e1ec190f-e3ce-490f-8a8c-5cd6f2d8167e WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/cbd465cb-51c4-40ce-816a-89e275982904 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/4d1b9f47-f73f-453b-ba58-65fa4a560ddd WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/35c3fdf1-2372-4518-9eda-da32cfc9f775 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/7fc8601f-afd5-4af3-baaf-0a042febb91b WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/2ec88ff3-cddd-47bd-8053-8a64132b22e5 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/7fca8369-4137-484d-acec-f3c75c0aae88 MSFragger [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3] java -jar -Dfile.encoding=UTF-8 -Xmx56G /home/nanopore-catalyst/fragpipe/tools/MSFragger-4.0/MSFragger-4.0.jar /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/fragger.params /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0000_1.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0000_2.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0000_3.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0000_4.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0030_1.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0030_2.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0030_3.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0030_4.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0090_1.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0090_2.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0090_3.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0090_4.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0000_1.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0000_2.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0000_3.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0000_4.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0015_1.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0015_2.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0015_3.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0015_4.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0060_1.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0060_2.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0060_3.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0060_4.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0000_1.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0000_2.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0000_3.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0000_4.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0030_1.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0030_2.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0030_3.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0030_4.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0090_1.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0090_2.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0090_3.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0090_4.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0000_1.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0000_2.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0015_1.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0015_2.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0015_3.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0015_4.raw MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0000_1.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1/CatA_0000_1.pepXML MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0000_1.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1/CatA_0000_1.pin MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0000_2.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_2/CatA_0000_2.pepXML MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0000_2.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_2/CatA_0000_2.pin MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0000_3.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_3/CatA_0000_3.pepXML MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0000_3.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_3/CatA_0000_3.pin MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0000_4.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_4/CatA_0000_4.pepXML MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0000_4.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_4/CatA_0000_4.pin MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0030_1.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_1/CatA_0030_1.pepXML MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0030_1.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_1/CatA_0030_1.pin MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0030_2.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_2/CatA_0030_2.pepXML MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0030_2.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_2/CatA_0030_2.pin MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0030_3.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_3/CatA_0030_3.pepXML MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0030_3.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_3/CatA_0030_3.pin MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0030_4.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_4/CatA_0030_4.pepXML MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0030_4.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_4/CatA_0030_4.pin MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0090_1.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_1/CatA_0090_1.pepXML MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0090_1.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_1/CatA_0090_1.pin MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0090_2.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_2/CatA_0090_2.pepXML MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0090_2.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_2/CatA_0090_2.pin MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0090_3.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_3/CatA_0090_3.pepXML MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0090_3.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_3/CatA_0090_3.pin MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0090_4.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_4/CatA_0090_4.pepXML MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0090_4.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_4/CatA_0090_4.pin MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0000_1.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_1/CatB_0000_1.pepXML MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0000_1.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_1/CatB_0000_1.pin MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0000_2.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_2/CatB_0000_2.pepXML MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0000_2.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_2/CatB_0000_2.pin MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0000_3.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_3/CatB_0000_3.pepXML MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0000_3.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_3/CatB_0000_3.pin MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0000_4.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_4/CatB_0000_4.pepXML MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0000_4.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_4/CatB_0000_4.pin MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0015_1.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_1/CatB_0015_1.pepXML MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0015_1.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_1/CatB_0015_1.pin MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0015_2.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_2/CatB_0015_2.pepXML MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0015_2.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_2/CatB_0015_2.pin MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0015_3.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_3/CatB_0015_3.pepXML MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0015_3.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_3/CatB_0015_3.pin MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0015_4.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_4/CatB_0015_4.pepXML MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0015_4.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_4/CatB_0015_4.pin MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0060_1.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_1/CatB_0060_1.pepXML MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0060_1.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_1/CatB_0060_1.pin MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0060_2.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_2/CatB_0060_2.pepXML MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0060_2.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_2/CatB_0060_2.pin MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0060_3.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_3/CatB_0060_3.pepXML MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0060_3.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_3/CatB_0060_3.pin MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0060_4.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_4/CatB_0060_4.pepXML MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0060_4.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_4/CatB_0060_4.pin MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0000_1.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_1/CatC_0000_1.pepXML MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0000_1.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_1/CatC_0000_1.pin MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0000_2.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_2/CatC_0000_2.pepXML MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0000_2.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_2/CatC_0000_2.pin MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0000_3.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_3/CatC_0000_3.pepXML MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0000_3.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_3/CatC_0000_3.pin MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0000_4.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_4/CatC_0000_4.pepXML MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0000_4.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_4/CatC_0000_4.pin MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0030_1.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_1/CatC_0030_1.pepXML MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0030_1.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_1/CatC_0030_1.pin MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0030_2.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_2/CatC_0030_2.pepXML MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0030_2.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_2/CatC_0030_2.pin MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0030_3.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_3/CatC_0030_3.pepXML MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0030_3.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_3/CatC_0030_3.pin MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0030_4.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_4/CatC_0030_4.pepXML MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0030_4.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_4/CatC_0030_4.pin MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0090_1.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_1/CatC_0090_1.pepXML MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0090_1.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_1/CatC_0090_1.pin MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0090_2.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_2/CatC_0090_2.pepXML MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0090_2.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_2/CatC_0090_2.pin MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0090_3.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_3/CatC_0090_3.pepXML MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0090_3.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_3/CatC_0090_3.pin MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0090_4.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_4/CatC_0090_4.pepXML MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0090_4.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_4/CatC_0090_4.pin MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0000_1.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0000_1/CatD_0000_1.pepXML MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0000_1.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0000_1/CatD_0000_1.pin MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0000_2.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0000_2/CatD_0000_2.pepXML MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0000_2.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0000_2/CatD_0000_2.pin MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0015_1.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_1/CatD_0015_1.pepXML MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0015_1.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_1/CatD_0015_1.pin MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0015_2.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_2/CatD_0015_2.pepXML MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0015_2.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_2/CatD_0015_2.pin MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0015_3.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_3/CatD_0015_3.pepXML MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0015_3.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_3/CatD_0015_3.pin MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0015_4.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_4/CatD_0015_4.pepXML MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0015_4.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_4/CatD_0015_4.pin MSBooster [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3] java -Xmx56G -cp /home/nanopore-catalyst/fragpipe/tools/msbooster-1.1.28.jar:/home/nanopore-catalyst/fragpipe/tools/batmass-io-1.30.0.jar Features.MainClass --paramsList /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/msbooster_params.txt Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_3] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatC_0090_3_percolator_target_psms.tsv --decoy-results-psms CatC_0090_3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatC_0090_3_edited.pin Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_4] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatA_0030_4_percolator_target_psms.tsv --decoy-results-psms CatA_0030_4_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatA_0030_4_edited.pin Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_2] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatC_0030_2_percolator_target_psms.tsv --decoy-results-psms CatC_0030_2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatC_0030_2_edited.pin Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_1] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatB_0015_1_percolator_target_psms.tsv --decoy-results-psms CatB_0015_1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatB_0015_1_edited.pin Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_4] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatC_0030_4_percolator_target_psms.tsv --decoy-results-psms CatC_0030_4_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatC_0030_4_edited.pin Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_2] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatA_0000_2_percolator_target_psms.tsv --decoy-results-psms CatA_0000_2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatA_0000_2_edited.pin Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_1] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatC_0090_1_percolator_target_psms.tsv --decoy-results-psms CatC_0090_1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatC_0090_1_edited.pin Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_1] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatB_0060_1_percolator_target_psms.tsv --decoy-results-psms CatB_0060_1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatB_0060_1_edited.pin Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_1] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatD_0015_1_percolator_target_psms.tsv --decoy-results-psms CatD_0015_1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatD_0015_1_edited.pin Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_1] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatA_0030_1_percolator_target_psms.tsv --decoy-results-psms CatA_0030_1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatA_0030_1_edited.pin Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_3] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatB_0000_3_percolator_target_psms.tsv --decoy-results-psms CatB_0000_3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatB_0000_3_edited.pin Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_2] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatA_0090_2_percolator_target_psms.tsv --decoy-results-psms CatA_0090_2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatA_0090_2_edited.pin Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_3] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatB_0060_3_percolator_target_psms.tsv --decoy-results-psms CatB_0060_3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatB_0060_3_edited.pin Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_4] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatD_0015_4_percolator_target_psms.tsv --decoy-results-psms CatD_0015_4_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatD_0015_4_edited.pin Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_2] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatA_0030_2_percolator_target_psms.tsv --decoy-results-psms CatA_0030_2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatA_0030_2_edited.pin Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_2] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatD_0015_2_percolator_target_psms.tsv --decoy-results-psms CatD_0015_2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatD_0015_2_edited.pin Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_3] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatA_0000_3_percolator_target_psms.tsv --decoy-results-psms CatA_0000_3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatA_0000_3_edited.pin Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_2] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatC_0090_2_percolator_target_psms.tsv --decoy-results-psms CatC_0090_2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatC_0090_2_edited.pin Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_3] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatC_0000_3_percolator_target_psms.tsv --decoy-results-psms CatC_0000_3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatC_0000_3_edited.pin Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatA_0000_1_percolator_target_psms.tsv --decoy-results-psms CatA_0000_1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatA_0000_1_edited.pin Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_4] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatC_0000_4_percolator_target_psms.tsv --decoy-results-psms CatC_0000_4_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatC_0000_4_edited.pin Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_2] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatB_0015_2_percolator_target_psms.tsv --decoy-results-psms CatB_0015_2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatB_0015_2_edited.pin Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_4] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatB_0015_4_percolator_target_psms.tsv --decoy-results-psms CatB_0015_4_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatB_0015_4_edited.pin Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_1] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatB_0000_1_percolator_target_psms.tsv --decoy-results-psms CatB_0000_1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatB_0000_1_edited.pin Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_1] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatA_0090_1_percolator_target_psms.tsv --decoy-results-psms CatA_0090_1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatA_0090_1_edited.pin Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_4] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatA_0090_4_percolator_target_psms.tsv --decoy-results-psms CatA_0090_4_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatA_0090_4_edited.pin Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_1] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatC_0000_1_percolator_target_psms.tsv --decoy-results-psms CatC_0000_1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatC_0000_1_edited.pin Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_1] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatC_0030_1_percolator_target_psms.tsv --decoy-results-psms CatC_0030_1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatC_0030_1_edited.pin Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_4] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatC_0090_4_percolator_target_psms.tsv --decoy-results-psms CatC_0090_4_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatC_0090_4_edited.pin Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_2] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatC_0000_2_percolator_target_psms.tsv --decoy-results-psms CatC_0000_2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatC_0000_2_edited.pin Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0000_1] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatD_0000_1_percolator_target_psms.tsv --decoy-results-psms CatD_0000_1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatD_0000_1_edited.pin Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_4] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatB_0060_4_percolator_target_psms.tsv --decoy-results-psms CatB_0060_4_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatB_0060_4_edited.pin Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_2] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatB_0000_2_percolator_target_psms.tsv --decoy-results-psms CatB_0000_2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatB_0000_2_edited.pin Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_4] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatA_0000_4_percolator_target_psms.tsv --decoy-results-psms CatA_0000_4_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatA_0000_4_edited.pin Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_4] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatB_0000_4_percolator_target_psms.tsv --decoy-results-psms CatB_0000_4_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatB_0000_4_edited.pin Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0000_2] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatD_0000_2_percolator_target_psms.tsv --decoy-results-psms CatD_0000_2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatD_0000_2_edited.pin Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_2] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatB_0060_2_percolator_target_psms.tsv --decoy-results-psms CatB_0060_2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatB_0060_2_edited.pin Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_3] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatA_0090_3_percolator_target_psms.tsv --decoy-results-psms CatA_0090_3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatA_0090_3_edited.pin Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_3] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatD_0015_3_percolator_target_psms.tsv --decoy-results-psms CatD_0015_3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatD_0015_3_edited.pin Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_3] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatC_0030_3_percolator_target_psms.tsv --decoy-results-psms CatC_0030_3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatC_0030_3_edited.pin Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_3] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatA_0030_3_percolator_target_psms.tsv --decoy-results-psms CatA_0030_3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatA_0030_3_edited.pin Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_3] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatB_0015_3_percolator_target_psms.tsv --decoy-results-psms CatB_0015_3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatB_0015_3_edited.pin Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_3] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatC_0090_3.pin CatC_0090_3 CatC_0090_3_percolator_target_psms.tsv CatC_0090_3_percolator_decoy_psms.tsv interact-CatC_0090_3 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0090_3_uncalibrated.mzML Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_3/CatC_0090_3_percolator_target_psms.tsv Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_3/CatC_0090_3_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_4] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatA_0030_4.pin CatA_0030_4 CatA_0030_4_percolator_target_psms.tsv CatA_0030_4_percolator_decoy_psms.tsv interact-CatA_0030_4 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0030_4_uncalibrated.mzML Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_4/CatA_0030_4_percolator_target_psms.tsv Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_4/CatA_0030_4_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_2] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatC_0030_2.pin CatC_0030_2 CatC_0030_2_percolator_target_psms.tsv CatC_0030_2_percolator_decoy_psms.tsv interact-CatC_0030_2 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0030_2_uncalibrated.mzML Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_2/CatC_0030_2_percolator_target_psms.tsv Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_2/CatC_0030_2_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_1] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatB_0015_1.pin CatB_0015_1 CatB_0015_1_percolator_target_psms.tsv CatB_0015_1_percolator_decoy_psms.tsv interact-CatB_0015_1 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0015_1_uncalibrated.mzML Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_1/CatB_0015_1_percolator_target_psms.tsv Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_1/CatB_0015_1_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_4] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatC_0030_4.pin CatC_0030_4 CatC_0030_4_percolator_target_psms.tsv CatC_0030_4_percolator_decoy_psms.tsv interact-CatC_0030_4 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0030_4_uncalibrated.mzML Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_4/CatC_0030_4_percolator_target_psms.tsv Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_4/CatC_0030_4_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_2] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatA_0000_2.pin CatA_0000_2 CatA_0000_2_percolator_target_psms.tsv CatA_0000_2_percolator_decoy_psms.tsv interact-CatA_0000_2 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0000_2_uncalibrated.mzML Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_2/CatA_0000_2_percolator_target_psms.tsv Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_2/CatA_0000_2_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_1] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatC_0090_1.pin CatC_0090_1 CatC_0090_1_percolator_target_psms.tsv CatC_0090_1_percolator_decoy_psms.tsv interact-CatC_0090_1 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0090_1_uncalibrated.mzML Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_1/CatC_0090_1_percolator_target_psms.tsv Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_1/CatC_0090_1_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_1] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatB_0060_1.pin CatB_0060_1 CatB_0060_1_percolator_target_psms.tsv CatB_0060_1_percolator_decoy_psms.tsv interact-CatB_0060_1 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0060_1_uncalibrated.mzML Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_1/CatB_0060_1_percolator_target_psms.tsv Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_1/CatB_0060_1_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_1] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatD_0015_1.pin CatD_0015_1 CatD_0015_1_percolator_target_psms.tsv CatD_0015_1_percolator_decoy_psms.tsv interact-CatD_0015_1 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0015_1_uncalibrated.mzML Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_1/CatD_0015_1_percolator_target_psms.tsv Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_1/CatD_0015_1_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_1] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatA_0030_1.pin CatA_0030_1 CatA_0030_1_percolator_target_psms.tsv CatA_0030_1_percolator_decoy_psms.tsv interact-CatA_0030_1 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0030_1_uncalibrated.mzML Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_1/CatA_0030_1_percolator_target_psms.tsv Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_1/CatA_0030_1_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_3] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatB_0000_3.pin CatB_0000_3 CatB_0000_3_percolator_target_psms.tsv CatB_0000_3_percolator_decoy_psms.tsv interact-CatB_0000_3 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0000_3_uncalibrated.mzML Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_3/CatB_0000_3_percolator_target_psms.tsv Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_3/CatB_0000_3_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_2] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatA_0090_2.pin CatA_0090_2 CatA_0090_2_percolator_target_psms.tsv CatA_0090_2_percolator_decoy_psms.tsv interact-CatA_0090_2 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0090_2_uncalibrated.mzML Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_2/CatA_0090_2_percolator_target_psms.tsv Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_2/CatA_0090_2_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_3] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatB_0060_3.pin CatB_0060_3 CatB_0060_3_percolator_target_psms.tsv CatB_0060_3_percolator_decoy_psms.tsv interact-CatB_0060_3 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0060_3_uncalibrated.mzML Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_3/CatB_0060_3_percolator_target_psms.tsv Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_3/CatB_0060_3_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_4] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatD_0015_4.pin CatD_0015_4 CatD_0015_4_percolator_target_psms.tsv CatD_0015_4_percolator_decoy_psms.tsv interact-CatD_0015_4 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0015_4_uncalibrated.mzML Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_4/CatD_0015_4_percolator_target_psms.tsv Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_4/CatD_0015_4_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_2] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatA_0030_2.pin CatA_0030_2 CatA_0030_2_percolator_target_psms.tsv CatA_0030_2_percolator_decoy_psms.tsv interact-CatA_0030_2 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0030_2_uncalibrated.mzML Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_2/CatA_0030_2_percolator_target_psms.tsv Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_2/CatA_0030_2_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_2] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatD_0015_2.pin CatD_0015_2 CatD_0015_2_percolator_target_psms.tsv CatD_0015_2_percolator_decoy_psms.tsv interact-CatD_0015_2 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0015_2_uncalibrated.mzML Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_2/CatD_0015_2_percolator_target_psms.tsv Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_2/CatD_0015_2_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_3] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatA_0000_3.pin CatA_0000_3 CatA_0000_3_percolator_target_psms.tsv CatA_0000_3_percolator_decoy_psms.tsv interact-CatA_0000_3 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0000_3_uncalibrated.mzML Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_3/CatA_0000_3_percolator_target_psms.tsv Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_3/CatA_0000_3_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_2] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatC_0090_2.pin CatC_0090_2 CatC_0090_2_percolator_target_psms.tsv CatC_0090_2_percolator_decoy_psms.tsv interact-CatC_0090_2 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0090_2_uncalibrated.mzML Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_2/CatC_0090_2_percolator_target_psms.tsv Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_2/CatC_0090_2_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_3] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatC_0000_3.pin CatC_0000_3 CatC_0000_3_percolator_target_psms.tsv CatC_0000_3_percolator_decoy_psms.tsv interact-CatC_0000_3 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0000_3_uncalibrated.mzML Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_3/CatC_0000_3_percolator_target_psms.tsv Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_3/CatC_0000_3_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatA_0000_1.pin CatA_0000_1 CatA_0000_1_percolator_target_psms.tsv CatA_0000_1_percolator_decoy_psms.tsv interact-CatA_0000_1 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0000_1_uncalibrated.mzML Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1/CatA_0000_1_percolator_target_psms.tsv Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1/CatA_0000_1_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_4] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatC_0000_4.pin CatC_0000_4 CatC_0000_4_percolator_target_psms.tsv CatC_0000_4_percolator_decoy_psms.tsv interact-CatC_0000_4 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0000_4_uncalibrated.mzML Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_4/CatC_0000_4_percolator_target_psms.tsv Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_4/CatC_0000_4_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_2] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatB_0015_2.pin CatB_0015_2 CatB_0015_2_percolator_target_psms.tsv CatB_0015_2_percolator_decoy_psms.tsv interact-CatB_0015_2 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0015_2_uncalibrated.mzML Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_2/CatB_0015_2_percolator_target_psms.tsv Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_2/CatB_0015_2_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_4] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatB_0015_4.pin CatB_0015_4 CatB_0015_4_percolator_target_psms.tsv CatB_0015_4_percolator_decoy_psms.tsv interact-CatB_0015_4 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0015_4_uncalibrated.mzML Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_4/CatB_0015_4_percolator_target_psms.tsv Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_4/CatB_0015_4_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_1] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatB_0000_1.pin CatB_0000_1 CatB_0000_1_percolator_target_psms.tsv CatB_0000_1_percolator_decoy_psms.tsv interact-CatB_0000_1 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0000_1_uncalibrated.mzML Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_1/CatB_0000_1_percolator_target_psms.tsv Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_1/CatB_0000_1_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_1] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatA_0090_1.pin CatA_0090_1 CatA_0090_1_percolator_target_psms.tsv CatA_0090_1_percolator_decoy_psms.tsv interact-CatA_0090_1 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0090_1_uncalibrated.mzML Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_1/CatA_0090_1_percolator_target_psms.tsv Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_1/CatA_0090_1_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_4] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatA_0090_4.pin CatA_0090_4 CatA_0090_4_percolator_target_psms.tsv CatA_0090_4_percolator_decoy_psms.tsv interact-CatA_0090_4 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0090_4_uncalibrated.mzML Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_4/CatA_0090_4_percolator_target_psms.tsv Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_4/CatA_0090_4_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_1] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatC_0000_1.pin CatC_0000_1 CatC_0000_1_percolator_target_psms.tsv CatC_0000_1_percolator_decoy_psms.tsv interact-CatC_0000_1 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0000_1_uncalibrated.mzML Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_1/CatC_0000_1_percolator_target_psms.tsv Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_1/CatC_0000_1_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_1] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatC_0030_1.pin CatC_0030_1 CatC_0030_1_percolator_target_psms.tsv CatC_0030_1_percolator_decoy_psms.tsv interact-CatC_0030_1 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0030_1_uncalibrated.mzML Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_1/CatC_0030_1_percolator_target_psms.tsv Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_1/CatC_0030_1_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_4] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatC_0090_4.pin CatC_0090_4 CatC_0090_4_percolator_target_psms.tsv CatC_0090_4_percolator_decoy_psms.tsv interact-CatC_0090_4 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0090_4_uncalibrated.mzML Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_4/CatC_0090_4_percolator_target_psms.tsv Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_4/CatC_0090_4_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_2] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatC_0000_2.pin CatC_0000_2 CatC_0000_2_percolator_target_psms.tsv CatC_0000_2_percolator_decoy_psms.tsv interact-CatC_0000_2 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0000_2_uncalibrated.mzML Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_2/CatC_0000_2_percolator_target_psms.tsv Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_2/CatC_0000_2_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0000_1] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatD_0000_1.pin CatD_0000_1 CatD_0000_1_percolator_target_psms.tsv CatD_0000_1_percolator_decoy_psms.tsv interact-CatD_0000_1 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0000_1_uncalibrated.mzML Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0000_1/CatD_0000_1_percolator_target_psms.tsv Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0000_1/CatD_0000_1_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_4] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatB_0060_4.pin CatB_0060_4 CatB_0060_4_percolator_target_psms.tsv CatB_0060_4_percolator_decoy_psms.tsv interact-CatB_0060_4 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0060_4_uncalibrated.mzML Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_4/CatB_0060_4_percolator_target_psms.tsv Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_4/CatB_0060_4_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_2] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatB_0000_2.pin CatB_0000_2 CatB_0000_2_percolator_target_psms.tsv CatB_0000_2_percolator_decoy_psms.tsv interact-CatB_0000_2 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0000_2_uncalibrated.mzML Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_2/CatB_0000_2_percolator_target_psms.tsv Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_2/CatB_0000_2_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_4] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatA_0000_4.pin CatA_0000_4 CatA_0000_4_percolator_target_psms.tsv CatA_0000_4_percolator_decoy_psms.tsv interact-CatA_0000_4 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0000_4_uncalibrated.mzML Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_4/CatA_0000_4_percolator_target_psms.tsv Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_4/CatA_0000_4_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_4] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatB_0000_4.pin CatB_0000_4 CatB_0000_4_percolator_target_psms.tsv CatB_0000_4_percolator_decoy_psms.tsv interact-CatB_0000_4 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0000_4_uncalibrated.mzML Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_4/CatB_0000_4_percolator_target_psms.tsv Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_4/CatB_0000_4_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0000_2] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatD_0000_2.pin CatD_0000_2 CatD_0000_2_percolator_target_psms.tsv CatD_0000_2_percolator_decoy_psms.tsv interact-CatD_0000_2 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0000_2_uncalibrated.mzML Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0000_2/CatD_0000_2_percolator_target_psms.tsv Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0000_2/CatD_0000_2_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_2] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatB_0060_2.pin CatB_0060_2 CatB_0060_2_percolator_target_psms.tsv CatB_0060_2_percolator_decoy_psms.tsv interact-CatB_0060_2 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0060_2_uncalibrated.mzML Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_2/CatB_0060_2_percolator_target_psms.tsv Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_2/CatB_0060_2_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_3] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatA_0090_3.pin CatA_0090_3 CatA_0090_3_percolator_target_psms.tsv CatA_0090_3_percolator_decoy_psms.tsv interact-CatA_0090_3 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0090_3_uncalibrated.mzML Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_3/CatA_0090_3_percolator_target_psms.tsv Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_3/CatA_0090_3_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_3] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatD_0015_3.pin CatD_0015_3 CatD_0015_3_percolator_target_psms.tsv CatD_0015_3_percolator_decoy_psms.tsv interact-CatD_0015_3 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0015_3_uncalibrated.mzML Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_3/CatD_0015_3_percolator_target_psms.tsv Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_3/CatD_0015_3_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_3] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatC_0030_3.pin CatC_0030_3 CatC_0030_3_percolator_target_psms.tsv CatC_0030_3_percolator_decoy_psms.tsv interact-CatC_0030_3 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0030_3_uncalibrated.mzML Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_3/CatC_0030_3_percolator_target_psms.tsv Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_3/CatC_0030_3_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_3] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatA_0030_3.pin CatA_0030_3 CatA_0030_3_percolator_target_psms.tsv CatA_0030_3_percolator_decoy_psms.tsv interact-CatA_0030_3 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0030_3_uncalibrated.mzML Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_3/CatA_0030_3_percolator_target_psms.tsv Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_3/CatA_0030_3_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_3] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatB_0015_3.pin CatB_0015_3 CatB_0015_3_percolator_target_psms.tsv CatB_0015_3_percolator_decoy_psms.tsv interact-CatB_0015_3 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0015_3_uncalibrated.mzML Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_3/CatB_0015_3_percolator_target_psms.tsv Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_3/CatB_0015_3_percolator_decoy_psms.tsv ProteinProphet [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher proteinprophet --maxppmdiff 2000000 --output combined /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/filelist_proteinprophet.txt PhilosopherDbAnnotate [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher database --annotate /home/nanopore-catalyst/centralized_files/proteome_databases/2024-09-16-decoys-contam-mspms_peptide_library.fasta.fas --prefix rev_ PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --razor PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_2 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_3 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_4 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_1 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_2 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_3 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_4 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_1 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_2 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_3 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_4 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_1 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_2 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_3 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_4 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_1 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_2 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_3 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_4 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_1 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_2 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_3 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_4 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_1 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_2 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_3 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_4 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_1 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_2 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_3 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_4 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_1 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_2 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_3 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_4 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0000_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0000_1 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0000_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0000_2 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_1 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_2 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_3 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_4 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0000_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0000_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0000_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0000_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck IonQuant [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3] java -Xmx56G -Dlibs.bruker.dir=/home/nanopore-catalyst/fragpipe/tools/MSFragger-4.0/ext/bruker -Dlibs.thermo.dir=/home/nanopore-catalyst/fragpipe/tools/MSFragger-4.0/ext/thermo -cp /home/nanopore-catalyst/fragpipe/tools/jfreechart-1.5.3.jar:/home/nanopore-catalyst/fragpipe/tools/batmass-io-1.30.0.jar:/home/nanopore-catalyst/fragpipe/tools/IonQuant-1.10.12.jar ionquant.IonQuant --threads 23 --perform-ms1quant 1 --perform-isoquant 0 --isotol 20.0 --isolevel 2 --isotype tmt10 --ionmobility 0 --site-reports 1 --minexps 1 --mbr 1 --maxlfq 1 --requantify 1 --mztol 10 --imtol 0.05 --rttol 0.4 --mbrmincorr 0 --mbrrttol 1 --mbrimtol 0.05 --mbrtoprun 15 --ionfdr 0.01 --proteinfdr 1 --peptidefdr 1 --normalization 1 --minisotopes 2 --minscans 3 --writeindex 0 --tp 0 --minfreq 0 --minions 2 --locprob 0.75 --uniqueness 0 --multidir . --filelist /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/filelist_ionquant.txt --modlist /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/modmasses_ionquant.txt ~~~~~~~~~~~~~~~~~~~~~~ Execution order: Cmd: [START], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3] Cmd: [CheckCentroid], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3] Cmd: [WorkspaceCleanInit], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_3] Cmd: [WorkspaceCleanInit], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_4] Cmd: [WorkspaceCleanInit], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_1] Cmd: [WorkspaceCleanInit], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_1] Cmd: [WorkspaceCleanInit], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_2] Cmd: [WorkspaceCleanInit], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_2] Cmd: [WorkspaceCleanInit], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_3] Cmd: [WorkspaceCleanInit], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_2] Cmd: [WorkspaceCleanInit], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_4] Cmd: [WorkspaceCleanInit], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_1] Cmd: [WorkspaceCleanInit], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_1] Cmd: [WorkspaceCleanInit], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_2] Cmd: [WorkspaceCleanInit], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_3] Cmd: [WorkspaceCleanInit], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_4] Cmd: [WorkspaceCleanInit], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_4] Cmd: [WorkspaceCleanInit], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_3] Cmd: [WorkspaceCleanInit], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_4] Cmd: [WorkspaceCleanInit], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_3] Cmd: [WorkspaceCleanInit], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_2] Cmd: [WorkspaceCleanInit], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1] Cmd: [WorkspaceCleanInit], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_2] Cmd: [WorkspaceCleanInit], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_1] Cmd: [WorkspaceCleanInit], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0000_1] Cmd: [WorkspaceCleanInit], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0000_2] Cmd: [WorkspaceCleanInit], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_4] Cmd: [WorkspaceCleanInit], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_1] Cmd: [WorkspaceCleanInit], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_3] Cmd: [WorkspaceCleanInit], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_1] Cmd: [WorkspaceCleanInit], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_3] Cmd: [WorkspaceCleanInit], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_2] Cmd: [WorkspaceCleanInit], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_2] Cmd: [WorkspaceCleanInit], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_3] Cmd: [WorkspaceCleanInit], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_4] Cmd: [WorkspaceCleanInit], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_4] Cmd: [WorkspaceCleanInit], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_4] Cmd: [WorkspaceCleanInit], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_3] Cmd: [WorkspaceCleanInit], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_4] Cmd: [WorkspaceCleanInit], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_3] Cmd: [WorkspaceCleanInit], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3] Cmd: [WorkspaceCleanInit], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_2] Cmd: [WorkspaceCleanInit], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_2] Cmd: [WorkspaceCleanInit], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_1] Cmd: [WorkspaceCleanInit], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_1] Cmd: [MSFragger], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3] Cmd: [MSBooster], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3] Cmd: [Percolator], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3] Cmd: [ProteinProphet], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3] Cmd: [PhilosopherDbAnnotate], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3] Cmd: [PhilosopherFilter], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3] Cmd: [PhilosopherReport], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3] Cmd: [WorkspaceClean], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_3] Cmd: [WorkspaceClean], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_4] Cmd: [WorkspaceClean], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_1] Cmd: [WorkspaceClean], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_1] Cmd: [WorkspaceClean], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_2] Cmd: [WorkspaceClean], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_2] Cmd: [WorkspaceClean], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_3] Cmd: [WorkspaceClean], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_2] Cmd: [WorkspaceClean], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_4] Cmd: [WorkspaceClean], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_1] Cmd: [WorkspaceClean], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_1] Cmd: [WorkspaceClean], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_2] Cmd: [WorkspaceClean], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_3] Cmd: [WorkspaceClean], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_4] Cmd: [WorkspaceClean], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_4] Cmd: [WorkspaceClean], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_3] Cmd: [WorkspaceClean], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_4] Cmd: [WorkspaceClean], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_3] Cmd: [WorkspaceClean], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_2] Cmd: [WorkspaceClean], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1] Cmd: [WorkspaceClean], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_2] Cmd: [WorkspaceClean], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_1] Cmd: [WorkspaceClean], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0000_1] Cmd: [WorkspaceClean], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0000_2] Cmd: [WorkspaceClean], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_4] Cmd: [WorkspaceClean], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_1] Cmd: [WorkspaceClean], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_3] Cmd: [WorkspaceClean], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_1] Cmd: [WorkspaceClean], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_3] Cmd: [WorkspaceClean], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_2] Cmd: [WorkspaceClean], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_2] Cmd: [WorkspaceClean], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_3] Cmd: [WorkspaceClean], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_4] Cmd: [WorkspaceClean], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_4] Cmd: [WorkspaceClean], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_4] Cmd: [WorkspaceClean], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_3] Cmd: [WorkspaceClean], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_4] Cmd: [WorkspaceClean], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_3] Cmd: [WorkspaceClean], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3] Cmd: [WorkspaceClean], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_2] Cmd: [WorkspaceClean], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_2] Cmd: [WorkspaceClean], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_1] Cmd: [WorkspaceClean], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_1] Cmd: [IonQuant], Work dir: [/home/nanopore-catalyst/HDD/mspms/fragpipe_out3] ~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~Sample of /home/nanopore-catalyst/centralized_files/proteome_databases/2024-09-16-decoys-contam-mspms_peptide_library.fasta.fas~~~~~~~ >TDP1 >TDP136 >TDP167 >TDP198 >TDP228 >TDP45 >TDP76 >rev_TDP109 >rev_TDP145 >rev_TDP176 >rev_TDP206 >rev_TDP237 >rev_TDP54 >rev_TDP86 >rev_sp|P00761|TRYP_PIG Trypsin OS=Sus scrofa OX=9823 PE=1 SV=1 >rev_sp|P02769|ALBU_BOVIN Albumin OS=Bos taurus OX=9913 GN=ALB PE=1 SV=4 >rev_sp|P41159|LEP_HUMAN Leptin OS=Homo sapiens OX=9606 GN=LEP PE=1 SV=1 >sp|O76013|KRT36_HUMAN Keratin, type I cuticular Ha6 OS=Homo sapiens OX=9606 GN=KRT36 PE=1 SV=1 >sp|P02438|KRB2A_SHEEP Keratin, high-sulfur matrix protein, B2A OS=Ovis aries OX=9940 PE=1 SV=2 >sp|P10145|IL8_HUMAN Interleukin-8 OS=Homo sapiens OX=9606 GN=CXCL8 PE=1 SV=1 >sp|Q06830|PRDX1_HUMAN Peroxiredoxin-1 OS=Homo sapiens OX=9606 GN=PRDX1 PE=1 SV=1 ~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~ fragpipe.config ~~~~~~~~~ # FragPipe v21.1ui state cache # Please edit the following path to point to the correct location. # In Windows, please replace single '\' with '\\' database.db-path=/home/nanopore-catalyst/centralized_files/proteome_databases/2024-09-16-decoys-contam-mspms_peptide_library.fasta.fas Table.editor=304.20715 crystalc.run-crystalc=false database.decoy-tag=rev_ diann.fragpipe.cmd-opts= diann.generate-msstats=true diann.heavy= diann.library= diann.light= diann.medium= diann.q-value=0.01 diann.quantification-strategy=3 diann.quantification-strategy-2=QuantUMS (high accuracy) diann.run-dia-nn=false diann.run-dia-plex=false diann.run-specific-protein-q-value=false diann.unrelated-runs=false diann.use-predicted-spectra=true diaumpire.AdjustFragIntensity=true diaumpire.BoostComplementaryIon=false diaumpire.CorrThreshold=0 diaumpire.DeltaApex=0.2 diaumpire.ExportPrecursorPeak=false diaumpire.Q1=true diaumpire.Q2=true diaumpire.Q3=true diaumpire.RFmax=500 diaumpire.RPmax=25 diaumpire.RTOverlap=0.3 diaumpire.SE.EstimateBG=false diaumpire.SE.IsoPattern=0.3 diaumpire.SE.MS1PPM=10 diaumpire.SE.MS2PPM=20 diaumpire.SE.MS2SN=1.1 diaumpire.SE.MassDefectFilter=true diaumpire.SE.MassDefectOffset=0.1 diaumpire.SE.NoMissedScan=1 diaumpire.SE.SN=1.1 diaumpire.run-diaumpire=false fpop.fpop-tmt=false fpop.label_control= fpop.label_fpop= fpop.region_size=1 fpop.run-fpop=false fpop.subtract-control=false fragpipe-config.bin-diann=/home/nanopore-catalyst/fragpipe/tools/diann/1.8.2_beta_8/linux/diann-1.8.1.8 fragpipe-config.bin-ionquant=/home/nanopore-catalyst/fragpipe/tools/IonQuant-1.10.12.jar fragpipe-config.bin-msfragger=/home/nanopore-catalyst/fragpipe/tools/MSFragger-4.0/MSFragger-4.0.jar fragpipe-config.bin-philosopher=/home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher fragpipe-config.bin-python=python freequant.mz-tol=10 freequant.rt-tol=0.4 freequant.run-freequant=false ionquant.excludemods= ionquant.heavy= ionquant.imtol=0.05 ionquant.ionfdr=0.01 ionquant.light= ionquant.locprob=0.75 ionquant.maxlfq=1 ionquant.mbr=1 ionquant.mbrimtol=0.05 ionquant.mbrmincorr=0 ionquant.mbrrttol=1 ionquant.mbrtoprun=15 ionquant.medium= ionquant.minfreq=0 ionquant.minions=2 ionquant.minisotopes=2 ionquant.minscans=3 ionquant.mztol=10 ionquant.normalization=1 ionquant.peptidefdr=1 ionquant.proteinfdr=1 ionquant.requantify=1 ionquant.rttol=0.4 ionquant.run-ionquant=true ionquant.tp=0 ionquant.uniqueness=0 ionquant.use-labeling=false ionquant.use-lfq=true ionquant.writeindex=0 msbooster.predict-rt=true msbooster.predict-spectra=true msbooster.run-msbooster=true msbooster.use-correlated-features=false msfragger.Y_type_masses= msfragger.activation_types=all msfragger.add_topN_complementary=0 msfragger.allowed_missed_cleavage_1=2 msfragger.allowed_missed_cleavage_2=2 msfragger.calibrate_mass=2 msfragger.check_spectral_files=true msfragger.clip_nTerm_M=true msfragger.deisotope=1 msfragger.delta_mass_exclude_ranges=(-1.5,3.5) msfragger.deneutralloss=1 msfragger.diagnostic_fragments= msfragger.diagnostic_intensity_filter=0 msfragger.digest_max_length=50 msfragger.digest_min_length=7 msfragger.fragment_ion_series=b,y msfragger.fragment_mass_tolerance=20 msfragger.fragment_mass_units=1 msfragger.group_variable=0 msfragger.intensity_transform=0 msfragger.ion_series_definitions= msfragger.isotope_error=0/1/2 msfragger.labile_search_mode=off msfragger.localize_delta_mass=false msfragger.mass_diff_to_variable_mod=0 msfragger.mass_offsets=0 msfragger.mass_offsets_detailed= msfragger.max_fragment_charge=2 msfragger.max_variable_mods_combinations=5000 msfragger.max_variable_mods_per_peptide=3 msfragger.min_fragments_modelling=2 msfragger.min_matched_fragments=4 msfragger.min_sequence_matches=2 msfragger.minimum_peaks=15 msfragger.minimum_ratio=0.01 msfragger.misc.fragger.clear-mz-hi=0 msfragger.misc.fragger.clear-mz-lo=0 msfragger.misc.fragger.digest-mass-hi=5000 msfragger.misc.fragger.digest-mass-lo=500 msfragger.misc.fragger.enzyme-dropdown-1=stricttrypsin msfragger.misc.fragger.enzyme-dropdown-2=null msfragger.misc.fragger.precursor-charge-hi=4 msfragger.misc.fragger.precursor-charge-lo=1 msfragger.misc.fragger.remove-precursor-range-hi=1.5 msfragger.misc.fragger.remove-precursor-range-lo=-1.5 msfragger.misc.slice-db=1 msfragger.num_enzyme_termini=0 msfragger.output_format=pepXML_pin msfragger.output_max_expect=50 msfragger.output_report_topN=1 msfragger.output_report_topN_dda_plus=5 msfragger.output_report_topN_dia1=5 msfragger.output_report_topN_dia2=3 msfragger.override_charge=false msfragger.precursor_mass_lower=-20 msfragger.precursor_mass_mode=selected msfragger.precursor_mass_units=1 msfragger.precursor_mass_upper=20 msfragger.precursor_true_tolerance=20 msfragger.precursor_true_units=1 msfragger.remainder_fragment_masses= msfragger.remove_precursor_peak=1 msfragger.report_alternative_proteins=true msfragger.require_precursor=true msfragger.restrict_deltamass_to=all msfragger.reuse_dia_fragment_peaks=false msfragger.run-msfragger=true msfragger.search_enzyme_cut_1=KR msfragger.search_enzyme_cut_2= msfragger.search_enzyme_name_1=stricttrypsin msfragger.search_enzyme_name_2=null msfragger.search_enzyme_nocut_1= msfragger.search_enzyme_nocut_2= msfragger.search_enzyme_sense_1=C msfragger.search_enzyme_sense_2=C msfragger.table.fix-mods=0.0,C-Term Peptide,true,-1; 0.0,N-Term Peptide,true,-1; 0.0,C-Term Protein,true,-1; 0.0,N-Term Protein,true,-1; 0.0,G (glycine),true,-1; 0.0,A (alanine),true,-1; 0.0,S (serine),true,-1; 0.0,P (proline),true,-1; 0.0,V (valine),true,-1; 0.0,T (threonine),true,-1; 57.02146,C (cysteine),true,-1; 0.0,L (leucine),true,-1; 0.0,I (isoleucine),true,-1; 0.0,N (asparagine),true,-1; 0.0,D (aspartic acid),true,-1; 0.0,Q (glutamine),true,-1; 0.0,K (lysine),true,-1; 0.0,E (glutamic acid),true,-1; 0.0,M (methionine),true,-1; 0.0,H (histidine),true,-1; 0.0,F (phenylalanine),true,-1; 0.0,R (arginine),true,-1; 0.0,Y (tyrosine),true,-1; 0.0,W (tryptophan),true,-1; 0.0,B ,true,-1; 0.0,J,true,-1; 0.0,O,true,-1; 0.0,U,true,-1; 0.0,X,true,-1; 0.0,Z,true,-1 msfragger.table.var-mods=15.9949,M,false,3; 42.0106,[^,false,1; 79.96633,STY,false,3; -17.0265,nQnC,false,1; -18.0106,nE,false,1; 4.025107,K,false,2; 6.020129,R,false,2; 8.014199,K,false,2; 10.008269,R,false,2; 0.0,site_10,false,1; 0.0,site_11,false,1; 0.0,site_12,false,1; 0.0,site_13,false,1; 0.0,site_14,false,1; 0.0,site_15,false,1; 0.0,site_16,false,1 msfragger.track_zero_topN=0 msfragger.use_all_mods_in_first_search=false msfragger.use_detailed_offsets=false msfragger.use_topN_peaks=150 msfragger.write_calibrated_mzml=false msfragger.write_uncalibrated_mgf=false msfragger.zero_bin_accept_expect=0 msfragger.zero_bin_mult_expect=1 opair.activation1=HCD opair.activation2=ETD opair.filterOxonium=true opair.glyco_db= opair.max_glycans=4 opair.max_isotope_error=2 opair.min_isotope_error=0 opair.ms1_tol=20 opair.ms2_tol=20 opair.oxonium_filtering_file= opair.oxonium_minimum_intensity=0.05 opair.reverse_scan_order=false opair.run-opair=false opair.single_scan_type=false peptide-prophet.cmd-opts=--decoyprobs --ppm --accmass --nonparam --expectscore peptide-prophet.combine-pepxml=false peptide-prophet.run-peptide-prophet=false percolator.cmd-opts=--only-psms --no-terminate --post-processing-tdc percolator.keep-tsv-files=false percolator.min-prob=0.5 percolator.run-percolator=true phi-report.dont-use-prot-proph-file=false phi-report.filter=--sequential --prot 0.01 phi-report.pep-level-summary=false phi-report.philosoher-msstats=false phi-report.print-decoys=false phi-report.prot-level-summary=false phi-report.remove-contaminants=false phi-report.run-report=true protein-prophet.cmd-opts=--maxppmdiff 2000000 protein-prophet.run-protein-prophet=true ptmprophet.cmdline=KEEPOLD STATIC EM\=1 NIONS\=b M\:15.9949,n\:42.0106 MINPROB\=0.5 ptmprophet.run-ptmprophet=false ptmshepherd.adv_params=false ptmshepherd.annotation-common=false ptmshepherd.annotation-custom=false ptmshepherd.annotation-glyco=false ptmshepherd.annotation-unimod=true ptmshepherd.annotation_file= ptmshepherd.annotation_tol=0.01 ptmshepherd.cap_y_ions= ptmshepherd.decoy_type=1 ptmshepherd.diag_ions= ptmshepherd.diagextract_mode=false ptmshepherd.diagmine_diagMinFoldChange=3.0 ptmshepherd.diagmine_diagMinSpecDiff=00.2 ptmshepherd.diagmine_fragMinFoldChange=3.0 ptmshepherd.diagmine_fragMinPropensity=00.1 ptmshepherd.diagmine_fragMinSpecDiff=00.1 ptmshepherd.diagmine_minIonsPerSpec=2 ptmshepherd.diagmine_minPeps=25 ptmshepherd.diagmine_mode=false ptmshepherd.diagmine_pepMinFoldChange=3.0 ptmshepherd.diagmine_pepMinSpecDiff=00.2 ptmshepherd.glyco_adducts= ptmshepherd.glyco_fdr=1.00 ptmshepherd.glyco_isotope_max=3 ptmshepherd.glyco_isotope_min=-1 ptmshepherd.glyco_mode=false ptmshepherd.glyco_ppm_tol=50 ptmshepherd.glycodatabase= ptmshepherd.histo_smoothbins=2 ptmshepherd.iontype_a=false ptmshepherd.iontype_b=true ptmshepherd.iontype_c=false ptmshepherd.iontype_x=false ptmshepherd.iontype_y=true ptmshepherd.iontype_z=false ptmshepherd.localization_allowed_res= ptmshepherd.localization_background=4 ptmshepherd.max_adducts=0 ptmshepherd.n_glyco=true ptmshepherd.normalization-psms=true ptmshepherd.normalization-scans=false ptmshepherd.output_extended=false ptmshepherd.peakpicking_mass_units=0 ptmshepherd.peakpicking_minPsm=10 ptmshepherd.peakpicking_promRatio=0.3 ptmshepherd.peakpicking_width=0.002 ptmshepherd.precursor_mass_units=0 ptmshepherd.precursor_tol=0.01 ptmshepherd.print_decoys=false ptmshepherd.prob_dhexOx=2,0.5,0.1 ptmshepherd.prob_dhexY=2,0.5 ptmshepherd.prob_neuacOx=2,0.05,0.2 ptmshepherd.prob_neugcOx=2,0.05,0.2 ptmshepherd.prob_phosphoOx=2,0.05,0.2 ptmshepherd.prob_regY=5,0.5 ptmshepherd.prob_sulfoOx=2,0.05,0.2 ptmshepherd.remainder_masses= ptmshepherd.remove_glycan_delta_mass=true ptmshepherd.run-shepherd=false ptmshepherd.run_diagextract_mode=false ptmshepherd.run_diagmine_mode=false ptmshepherd.run_glyco_mode=false ptmshepherd.spectra_maxfragcharge=2 ptmshepherd.spectra_ppmtol=20 ptmshepherd.varmod_masses= quantitation.run-label-free-quant=true run-psm-validation=true run-validation-tab=true saintexpress.fragpipe.cmd-opts= saintexpress.max-replicates=10 saintexpress.run-saint-express=false saintexpress.virtual-controls=100 speclibgen.easypqp.extras.max_delta_ppm=15 speclibgen.easypqp.extras.max_delta_unimod=0.02 speclibgen.easypqp.extras.rt_lowess_fraction=0 speclibgen.easypqp.fragment.a=false speclibgen.easypqp.fragment.b=true speclibgen.easypqp.fragment.c=false speclibgen.easypqp.fragment.x=false speclibgen.easypqp.fragment.y=true speclibgen.easypqp.fragment.z=false speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM speclibgen.easypqp.neutral_loss=false speclibgen.easypqp.rt-cal=noiRT speclibgen.easypqp.select-file.text= speclibgen.easypqp.select-im-file.text= speclibgen.keep-intermediate-files=false speclibgen.run-speclibgen=false tab-run.delete_calibrated_mzml=false tab-run.delete_temp_files=false tab-run.sub_mzml_prob_threshold=0.5 tab-run.write_sub_mzml=false tmtintegrator.add_Ref=-1 tmtintegrator.aggregation_method=0 tmtintegrator.allow_overlabel=true tmtintegrator.allow_unlabeled=true tmtintegrator.best_psm=true tmtintegrator.channel_num=TMT-6 tmtintegrator.dont-run-fq-lq=false tmtintegrator.extraction_tool=IonQuant tmtintegrator.glyco_qval=-1 tmtintegrator.groupby=0 tmtintegrator.log2transformed=true tmtintegrator.max_pep_prob_thres=0 tmtintegrator.min_ntt=0 tmtintegrator.min_pep_prob=0.9 tmtintegrator.min_percent=0.05 tmtintegrator.min_purity=0.5 tmtintegrator.min_site_prob=-1 tmtintegrator.mod_tag=none tmtintegrator.ms1_int=true tmtintegrator.outlier_removal=true tmtintegrator.print_RefInt=false tmtintegrator.prot_exclude=none tmtintegrator.prot_norm=0 tmtintegrator.psm_norm=false tmtintegrator.quant_level=2 tmtintegrator.ref_tag=Bridge tmtintegrator.run-tmtintegrator=false tmtintegrator.tolerance=20 tmtintegrator.top3_pep=true tmtintegrator.unique_gene=0 tmtintegrator.unique_pep=false tmtintegrator.use_glycan_composition=false workdir=/home/nanopore-catalyst/HDD/mspms/fragpipe_out3 workflow.input.data-type.im-ms=false workflow.input.data-type.regular-ms=true workflow.misc.save-sdrf=true workflow.ram=0 workflow.threads=23 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CheckCentroid java -Xmx56G -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/tools/batmass-io-1.30.0.jar com.dmtavt.fragpipe.util.CheckCentroid /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0000_1.raw 23 Done in 0.0 s. Process 'CheckCentroid' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="17:57:20" level=info msg="Executing Workspace v5.1.0" time="17:57:20" level=info msg="Removing workspace" time="17:57:20" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/ce4d5a4b-7c25-4981-8658-3a9ef82d46bd time="17:57:20" level=info msg="Executing Workspace v5.1.0" time="17:57:20" level=info msg="Creating workspace" time="17:57:20" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="17:57:20" level=info msg="Executing Workspace v5.1.0" time="17:57:20" level=info msg="Removing workspace" time="17:57:20" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/5787929d-c2f8-4a5f-a975-86ec494f8f3c time="17:57:20" level=info msg="Executing Workspace v5.1.0" time="17:57:20" level=info msg="Creating workspace" time="17:57:20" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="17:57:20" level=info msg="Executing Workspace v5.1.0" time="17:57:20" level=info msg="Removing workspace" time="17:57:20" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/99347bc6-617b-48b3-9430-7360063e3646 time="17:57:21" level=info msg="Executing Workspace v5.1.0" time="17:57:21" level=info msg="Creating workspace" time="17:57:21" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="17:57:21" level=info msg="Executing Workspace v5.1.0" time="17:57:21" level=info msg="Removing workspace" time="17:57:21" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/43fb631b-845b-4b97-9f86-d6b0aa80f423 time="17:57:21" level=info msg="Executing Workspace v5.1.0" time="17:57:21" level=info msg="Creating workspace" time="17:57:21" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="17:57:21" level=info msg="Executing Workspace v5.1.0" time="17:57:21" level=info msg="Removing workspace" time="17:57:21" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/5c52d430-2d67-467b-a881-4dcc93bd6d63 time="17:57:21" level=info msg="Executing Workspace v5.1.0" time="17:57:21" level=info msg="Creating workspace" time="17:57:22" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="17:57:22" level=info msg="Executing Workspace v5.1.0" time="17:57:22" level=info msg="Removing workspace" time="17:57:22" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/1da1a03b-1800-45d7-b50e-17e3ce7af667 time="17:57:22" level=info msg="Executing Workspace v5.1.0" time="17:57:22" level=info msg="Creating workspace" time="17:57:22" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="17:57:22" level=info msg="Executing Workspace v5.1.0" time="17:57:22" level=info msg="Removing workspace" time="17:57:22" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/fc6b848f-b734-4a53-bf8a-a4c312532ee7 time="17:57:22" level=info msg="Executing Workspace v5.1.0" time="17:57:22" level=info msg="Creating workspace" time="17:57:22" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="17:57:22" level=info msg="Executing Workspace v5.1.0" time="17:57:22" level=info msg="Removing workspace" time="17:57:22" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/1204c0bb-3cbe-445f-b42d-395578f716c4 time="17:57:23" level=info msg="Executing Workspace v5.1.0" time="17:57:23" level=info msg="Creating workspace" time="17:57:23" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="17:57:23" level=info msg="Executing Workspace v5.1.0" time="17:57:23" level=info msg="Removing workspace" time="17:57:23" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/b6793aed-7f17-4fc9-9935-faa36f11ce97 time="17:57:23" level=info msg="Executing Workspace v5.1.0" time="17:57:23" level=info msg="Creating workspace" time="17:57:23" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="17:57:23" level=info msg="Executing Workspace v5.1.0" time="17:57:23" level=info msg="Removing workspace" time="17:57:23" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/0e5d87de-a9ac-4747-8d3d-d42d4fdff3e3 time="17:57:24" level=info msg="Executing Workspace v5.1.0" time="17:57:24" level=info msg="Creating workspace" time="17:57:24" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="17:57:24" level=info msg="Executing Workspace v5.1.0" time="17:57:24" level=info msg="Removing workspace" time="17:57:24" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/87f586d6-7c14-4842-87d2-8c83edd7ae45 time="17:57:24" level=info msg="Executing Workspace v5.1.0" time="17:57:24" level=info msg="Creating workspace" time="17:57:24" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="17:57:24" level=info msg="Executing Workspace v5.1.0" time="17:57:24" level=info msg="Removing workspace" time="17:57:24" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/1b4f5fe5-16b0-48c8-a198-c6d0e85fc308 time="17:57:24" level=info msg="Executing Workspace v5.1.0" time="17:57:24" level=info msg="Creating workspace" time="17:57:24" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="17:57:25" level=info msg="Executing Workspace v5.1.0" time="17:57:25" level=info msg="Removing workspace" time="17:57:25" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/473986bb-96e0-440d-87d5-cc9e29c822d0 time="17:57:25" level=info msg="Executing Workspace v5.1.0" time="17:57:25" level=info msg="Creating workspace" time="17:57:25" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="17:57:25" level=info msg="Executing Workspace v5.1.0" time="17:57:25" level=info msg="Removing workspace" time="17:57:25" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/9d05af0f-b5af-4572-af95-a9efad0dafe0 time="17:57:25" level=info msg="Executing Workspace v5.1.0" time="17:57:25" level=info msg="Creating workspace" time="17:57:25" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="17:57:25" level=info msg="Executing Workspace v5.1.0" time="17:57:25" level=info msg="Removing workspace" time="17:57:25" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/d38f0150-a938-4177-9155-b9fc21f95a01 time="17:57:26" level=info msg="Executing Workspace v5.1.0" time="17:57:26" level=info msg="Creating workspace" time="17:57:26" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="17:57:26" level=info msg="Executing Workspace v5.1.0" time="17:57:26" level=info msg="Removing workspace" time="17:57:26" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/0c4ec3ac-186f-43b1-85e9-a98cdc3b40ea time="17:57:26" level=info msg="Executing Workspace v5.1.0" time="17:57:26" level=info msg="Creating workspace" time="17:57:26" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="17:57:26" level=info msg="Executing Workspace v5.1.0" time="17:57:26" level=info msg="Removing workspace" time="17:57:26" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/455b595e-8ee9-4930-8e26-56c68a8585e0 time="17:57:26" level=info msg="Executing Workspace v5.1.0" time="17:57:26" level=info msg="Creating workspace" time="17:57:26" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="17:57:27" level=info msg="Executing Workspace v5.1.0" time="17:57:27" level=info msg="Removing workspace" time="17:57:27" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/3c931408-69fe-401c-8dad-8493085b210d time="17:57:27" level=info msg="Executing Workspace v5.1.0" time="17:57:27" level=info msg="Creating workspace" time="17:57:27" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="17:57:27" level=info msg="Executing Workspace v5.1.0" time="17:57:27" level=info msg="Removing workspace" time="17:57:27" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/38cdd109-15af-48bf-8c83-79370e97d897 time="17:57:27" level=info msg="Executing Workspace v5.1.0" time="17:57:27" level=info msg="Creating workspace" time="17:57:27" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="17:57:27" level=info msg="Executing Workspace v5.1.0" time="17:57:27" level=info msg="Removing workspace" time="17:57:27" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/fa351ef3-e932-42e9-89e7-d90b1959fa3a time="17:57:28" level=info msg="Executing Workspace v5.1.0" time="17:57:28" level=info msg="Creating workspace" time="17:57:28" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="17:57:28" level=info msg="Executing Workspace v5.1.0" time="17:57:28" level=info msg="Removing workspace" time="17:57:28" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/9eb5deff-fe65-476d-8f8b-30ddc64e7676 time="17:57:28" level=info msg="Executing Workspace v5.1.0" time="17:57:28" level=info msg="Creating workspace" time="17:57:28" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="17:57:28" level=info msg="Executing Workspace v5.1.0" time="17:57:28" level=info msg="Removing workspace" time="17:57:28" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/4ec418cb-4f5e-43bb-86bb-f92cdfa9820b time="17:57:28" level=info msg="Executing Workspace v5.1.0" time="17:57:28" level=info msg="Creating workspace" time="17:57:28" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0000_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="17:57:29" level=info msg="Executing Workspace v5.1.0" time="17:57:29" level=info msg="Removing workspace" time="17:57:29" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0000_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/e5b06af0-c0e1-433b-8678-4a1ab86f80bc time="17:57:29" level=info msg="Executing Workspace v5.1.0" time="17:57:29" level=info msg="Creating workspace" time="17:57:29" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0000_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="17:57:29" level=info msg="Executing Workspace v5.1.0" time="17:57:29" level=info msg="Removing workspace" time="17:57:29" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0000_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/64b0412e-129c-4db1-86ec-c782657b76d4 time="17:57:29" level=info msg="Executing Workspace v5.1.0" time="17:57:29" level=info msg="Creating workspace" time="17:57:29" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="17:57:29" level=info msg="Executing Workspace v5.1.0" time="17:57:29" level=info msg="Removing workspace" time="17:57:29" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/041aa3fa-2317-4a5b-b08c-5e517c79ab8c time="17:57:30" level=info msg="Executing Workspace v5.1.0" time="17:57:30" level=info msg="Creating workspace" time="17:57:30" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="17:57:30" level=info msg="Executing Workspace v5.1.0" time="17:57:30" level=info msg="Removing workspace" time="17:57:30" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/2185cb32-4c72-461d-8cf1-4b32b3a2a1f4 time="17:57:30" level=info msg="Executing Workspace v5.1.0" time="17:57:30" level=info msg="Creating workspace" time="17:57:30" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="17:57:30" level=info msg="Executing Workspace v5.1.0" time="17:57:30" level=info msg="Removing workspace" time="17:57:30" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/662ce773-19cf-4eb6-96d7-3cf5b553b345 time="17:57:30" level=info msg="Executing Workspace v5.1.0" time="17:57:30" level=info msg="Creating workspace" time="17:57:31" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="17:57:31" level=info msg="Executing Workspace v5.1.0" time="17:57:31" level=info msg="Removing workspace" time="17:57:31" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/10eba5ff-5dc3-407a-ade1-fdb03f52a678 time="17:57:31" level=info msg="Executing Workspace v5.1.0" time="17:57:31" level=info msg="Creating workspace" time="17:57:31" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="17:57:31" level=info msg="Executing Workspace v5.1.0" time="17:57:31" level=info msg="Removing workspace" time="17:57:31" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/bf613636-b982-47c5-84a8-2482f1efdbab time="17:57:31" level=info msg="Executing Workspace v5.1.0" time="17:57:31" level=info msg="Creating workspace" time="17:57:31" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="17:57:31" level=info msg="Executing Workspace v5.1.0" time="17:57:31" level=info msg="Removing workspace" time="17:57:31" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/fcf7c3b0-d20f-43ef-b05c-d20493b794b0 time="17:57:32" level=info msg="Executing Workspace v5.1.0" time="17:57:32" level=info msg="Creating workspace" time="17:57:32" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="17:57:32" level=info msg="Executing Workspace v5.1.0" time="17:57:32" level=info msg="Removing workspace" time="17:57:32" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/c41b1b55-aa88-4980-bb47-305e289b05d2 time="17:57:32" level=info msg="Executing Workspace v5.1.0" time="17:57:32" level=info msg="Creating workspace" time="17:57:32" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="17:57:32" level=info msg="Executing Workspace v5.1.0" time="17:57:32" level=info msg="Removing workspace" time="17:57:32" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/611c8b54-552a-431c-bd2b-f956e593b575 time="17:57:32" level=info msg="Executing Workspace v5.1.0" time="17:57:32" level=info msg="Creating workspace" time="17:57:33" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="17:57:33" level=info msg="Executing Workspace v5.1.0" time="17:57:33" level=info msg="Removing workspace" time="17:57:33" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/d9f9550b-7cfa-4203-874b-2ce8aa42cfb4 time="17:57:33" level=info msg="Executing Workspace v5.1.0" time="17:57:33" level=info msg="Creating workspace" time="17:57:33" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="17:57:33" level=info msg="Executing Workspace v5.1.0" time="17:57:33" level=info msg="Removing workspace" time="17:57:33" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/6f8326f7-69a9-40c8-ab37-2baa2656edfe time="17:57:33" level=info msg="Executing Workspace v5.1.0" time="17:57:33" level=info msg="Creating workspace" time="17:57:33" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="17:57:34" level=info msg="Executing Workspace v5.1.0" time="17:57:34" level=info msg="Removing workspace" time="17:57:34" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/08409ab1-e96f-4aad-8052-9680f72e2a0a time="17:57:34" level=info msg="Executing Workspace v5.1.0" time="17:57:34" level=info msg="Creating workspace" time="17:57:34" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="17:57:34" level=info msg="Executing Workspace v5.1.0" time="17:57:34" level=info msg="Removing workspace" time="17:57:34" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/70f75b0b-ad72-4518-9d96-3d0ff16508f8 time="17:57:34" level=info msg="Executing Workspace v5.1.0" time="17:57:34" level=info msg="Creating workspace" time="17:57:34" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="17:57:34" level=info msg="Executing Workspace v5.1.0" time="17:57:34" level=info msg="Removing workspace" time="17:57:34" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/e1ec190f-e3ce-490f-8a8c-5cd6f2d8167e time="17:57:35" level=info msg="Executing Workspace v5.1.0" time="17:57:35" level=info msg="Creating workspace" time="17:57:35" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="17:57:35" level=info msg="Executing Workspace v5.1.0" time="17:57:35" level=info msg="Removing workspace" time="17:57:35" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/cbd465cb-51c4-40ce-816a-89e275982904 time="17:57:35" level=info msg="Executing Workspace v5.1.0" time="17:57:35" level=info msg="Creating workspace" time="17:57:35" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="17:57:35" level=info msg="Executing Workspace v5.1.0" time="17:57:35" level=info msg="Removing workspace" time="17:57:35" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/4d1b9f47-f73f-453b-ba58-65fa4a560ddd time="17:57:35" level=info msg="Executing Workspace v5.1.0" time="17:57:35" level=info msg="Creating workspace" time="17:57:35" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="17:57:36" level=info msg="Executing Workspace v5.1.0" time="17:57:36" level=info msg="Removing workspace" time="17:57:36" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/35c3fdf1-2372-4518-9eda-da32cfc9f775 time="17:57:36" level=info msg="Executing Workspace v5.1.0" time="17:57:36" level=info msg="Creating workspace" time="17:57:36" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="17:57:36" level=info msg="Executing Workspace v5.1.0" time="17:57:36" level=info msg="Removing workspace" time="17:57:36" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/7fc8601f-afd5-4af3-baaf-0a042febb91b time="17:57:36" level=info msg="Executing Workspace v5.1.0" time="17:57:36" level=info msg="Creating workspace" time="17:57:36" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="17:57:36" level=info msg="Executing Workspace v5.1.0" time="17:57:36" level=info msg="Removing workspace" time="17:57:36" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/2ec88ff3-cddd-47bd-8053-8a64132b22e5 time="17:57:37" level=info msg="Executing Workspace v5.1.0" time="17:57:37" level=info msg="Creating workspace" time="17:57:37" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="17:57:37" level=info msg="Executing Workspace v5.1.0" time="17:57:37" level=info msg="Removing workspace" time="17:57:37" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/7fca8369-4137-484d-acec-f3c75c0aae88 time="17:57:37" level=info msg="Executing Workspace v5.1.0" time="17:57:37" level=info msg="Creating workspace" time="17:57:37" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 MSFragger [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3] java -jar -Dfile.encoding=UTF-8 -Xmx56G /home/nanopore-catalyst/fragpipe/tools/MSFragger-4.0/MSFragger-4.0.jar /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/fragger.params /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0000_1.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0000_2.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0000_3.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0000_4.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0030_1.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0030_2.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0030_3.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0030_4.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0090_1.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0090_2.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0090_3.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0090_4.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0000_1.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0000_2.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0000_3.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0000_4.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0015_1.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0015_2.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0015_3.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0015_4.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0060_1.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0060_2.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0060_3.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0060_4.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0000_1.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0000_2.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0000_3.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0000_4.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0030_1.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0030_2.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0030_3.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0030_4.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0090_1.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0090_2.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0090_3.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0090_4.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0000_1.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0000_2.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0015_1.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0015_2.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0015_3.raw /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0015_4.raw MSFragger version MSFragger-4.0 Batmass-IO version 1.30.0 timsdata library version timsdata-2-21-0-4 (c) University of Michigan RawFileReader reading tool. Copyright (c) 2016 by Thermo Fisher Scientific, Inc. All rights reserved. timdTOF .d reading tool. Copyright (c) 2022 by Bruker Daltonics GmbH & Co. KG. All rights reserved. System OS: Linux, Architecture: amd64 Java Info: 11.0.23, OpenJDK 64-Bit Server VM, Ubuntu JVM started with 56 GB memory Checking database... Checking spectral files... /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0030_2.raw: Scans = 31365; Isolation sizes = [1.5] /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0000_1.raw: Scans = 33081; Isolation sizes = [1.5] /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0060_2.raw: Scans = 34266; Isolation sizes = [1.5] /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0090_3.raw: Scans = 30581; Isolation sizes = [1.5] /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0030_4.raw: Scans = 33775; Isolation sizes = [1.5] /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0000_1.raw: Scans = 32626; Isolation sizes = [1.5] /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0000_4.raw: Scans = 34884; Isolation sizes = [1.5] /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0000_3.raw: Scans = 33852; Isolation sizes = [1.5] /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0000_2.raw: Scans = 33242; Isolation sizes = [1.5] /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0030_3.raw: Scans = 31788; Isolation sizes = [1.5] /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0090_4.raw: Scans = 30349; Isolation sizes = [1.5] /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0000_2.raw: Scans = 31440; Isolation sizes = [1.5] /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0060_3.raw: Scans = 34445; Isolation sizes = [1.5] /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0090_1.raw: Scans = 33711; Isolation sizes = [1.5] /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0015_1.raw: Scans = 34788; Isolation sizes = [1.5] /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0000_4.raw: Scans = 33912; Isolation sizes = [1.5] /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0015_1.raw: Scans = 33699; Isolation sizes = [1.5] /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0030_4.raw: Scans = 32507; Isolation sizes = [1.5] /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0000_1.raw: Scans = 34917; Isolation sizes = [1.5] /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0000_3.raw: Scans = 32113; Isolation sizes = [1.5] /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0030_1.raw: Scans = 33638; Isolation sizes = [1.5] /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0060_4.raw: Scans = 34039; Isolation sizes = [1.5] /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0015_2.raw: Scans = 35398; Isolation sizes = [1.5] /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0090_2.raw: Scans = 34238; Isolation sizes = [1.5] /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0015_2.raw: Scans = 33093; Isolation sizes = [1.5] /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0090_1.raw: Scans = 31232; Isolation sizes = [1.5] /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0000_4.raw: Scans = 32492; Isolation sizes = [1.5] /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0000_2.raw: Scans = 34092; Isolation sizes = [1.5] /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0030_2.raw: Scans = 33677; Isolation sizes = [1.5] /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0000_1.raw: Scans = 34015; Isolation sizes = [1.5] /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0015_3.raw: Scans = 34643; Isolation sizes = [1.5] /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0090_3.raw: Scans = 33937; Isolation sizes = [1.5] /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0015_3.raw: Scans = 33875; Isolation sizes = [1.5] /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0090_2.raw: Scans = 30982; Isolation sizes = [1.5] /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0030_1.raw: Scans = 31584; Isolation sizes = [1.5] /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0000_3.raw: Scans = 34732; Isolation sizes = [1.5] /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0030_3.raw: Scans = 33888; Isolation sizes = [1.5] /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0000_2.raw: Scans = 34170; Isolation sizes = [1.5] /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0090_4.raw: Scans = 34438; Isolation sizes = [1.5] /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0015_4.raw: Scans = 34355; Isolation sizes = [1.5] /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0015_4.raw: Scans = 33397; Isolation sizes = [1.5] /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0060_1.raw: Scans = 34681; Isolation sizes = [1.5] ***********************************FIRST SEARCH************************************ Parameters: num_threads = 23 database_name = /home/nanopore-catalyst/centralized_files/proteome_databases/2024-09-16-decoys-contam-mspms_peptide_library.fasta.fas decoy_prefix = rev_ precursor_mass_lower = -20.0 precursor_mass_upper = 20.0 precursor_mass_units = 1 data_type = 0 precursor_true_tolerance = 20.0 precursor_true_units = 1 fragment_mass_tolerance = 20.0 fragment_mass_units = 1 calibrate_mass = 2 use_all_mods_in_first_search = 0 write_calibrated_mzml = 0 write_uncalibrated_mgf = 0 write_mzbin_all = 0 isotope_error = 0 mass_offsets = 0 labile_search_mode = OFF restrict_deltamass_to = all precursor_mass_mode = SELECTED localize_delta_mass = 0 delta_mass_exclude_ranges = (-1.5,3.5) fragment_ion_series = b,y ion_series_definitions = search_enzyme_name = stricttrypsin search_enzyme_sense_1 = C search_enzyme_cut_1 = KR search_enzyme_nocut_1 = allowed_missed_cleavage_1 = 2 num_enzyme_termini = 0 clip_nTerm_M = 1 allow_multiple_variable_mods_on_residue = 0 max_variable_mods_per_peptide = 3 max_variable_mods_combinations = 5000 output_format = pepxml_pin output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = 0 override_charge = 0 precursor_charge_low = 2 precursor_charge_high = 3 digest_min_length = 8 digest_max_length = 15 digest_mass_range_low = 500.0 digest_mass_range_high = 5000.0 max_fragment_charge = 1 deisotope = 1 deneutralloss = 1 track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 minimum_peaks = 15 use_topN_peaks = 150 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.01 intensity_transform = 0 activation_types = all group_variable = 0 require_precursor = 1 reuse_dia_fragment_peaks = 0 remove_precursor_peak = 1 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 0.0 clear_mz_range_high = 0.0 excluded_scan_list_file = mass_diff_to_variable_mod = 0 min_sequence_matches = 2 check_spectral_files = 1 add_A_alanine = 0.0 add_B_user_amino_acid = 0.0 add_C_cysteine = 57.02146 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.0 add_E_glutamic_acid = 0.0 add_F_phenylalanine = 0.0 add_G_glycine = 0.0 add_H_histidine = 0.0 add_I_isoleucine = 0.0 add_J_user_amino_acid = 0.0 add_K_lysine = 0.0 add_L_leucine = 0.0 add_M_methionine = 0.0 add_N_asparagine = 0.0 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.0 # O = pyrrolysine (237.14773 Da) add_P_proline = 0.0 add_Q_glutamine = 0.0 add_R_arginine = 0.0 add_S_serine = 0.0 add_T_threonine = 0.0 add_U_user_amino_acid = 0.0 # U = selenocysteine (150.95363 Da) add_V_valine = 0.0 add_W_tryptophan = 0.0 add_X_user_amino_acid = 0.0 add_Y_tyrosine = 0.0 add_Z_user_amino_acid = 0.0 Selected fragment index width 0.10 Da. 11340542 fragments to be searched in 1 slices (0.17 GB total) Operating on slice 1 of 1: Fragment index slice generated in 0.25 s 001. CatA_0000_1.raw 5.9 s | deisotoping 0.5 s [progress: 24730/24730 (100%) - 22461 spectra/s] 1.1s | postprocessing 0.0 s 002. CatA_0000_2.raw 5.2 s | deisotoping 0.0 s [progress: 23432/23432 (100%) - 234320 spectra/s] 0.1s | postprocessing 0.0 s 003. CatA_0000_3.raw 5.2 s | deisotoping 0.0 s [progress: 24627/24627 (100%) - 246270 spectra/s] 0.1s | postprocessing 0.0 s 004. CatA_0000_4.raw 5.2 s | deisotoping 0.0 s [progress: 24944/24944 (100%) - 249440 spectra/s] 0.1s | postprocessing 0.0 s 005. CatA_0030_1.raw 5.0 s | deisotoping 0.0 s [progress: 22989/22989 (100%) - 229890 spectra/s] 0.1s | postprocessing 0.0 s 006. CatA_0030_2.raw 5.1 s | deisotoping 0.0 s [progress: 22379/22379 (100%) - 221574 spectra/s] 0.1s | postprocessing 0.0 s 007. CatA_0030_3.raw 5.3 s | deisotoping 0.0 s [progress: 22817/22817 (100%) - 228170 spectra/s] 0.1s | postprocessing 0.0 s 008. CatA_0030_4.raw 5.5 s | deisotoping 0.0 s [progress: 24447/24447 (100%) - 242050 spectra/s] 0.1s | postprocessing 0.0 s 009. CatA_0090_1.raw 5.1 s | deisotoping 0.0 s [progress: 22229/22229 (100%) - 111145 spectra/s] 0.2s | postprocessing 0.0 s 010. CatA_0090_2.raw 9.6 s | deisotoping 0.0 s [progress: 22198/22198 (100%) - 221980 spectra/s] 0.1s | postprocessing 0.0 s 011. CatA_0090_3.raw 9.3 s | deisotoping 0.0 s [progress: 23613/23613 (100%) - 236130 spectra/s] 0.1s | postprocessing 0.0 s 012. CatA_0090_4.raw 9.2 s | deisotoping 0.0 s [progress: 23470/23470 (100%) - 234700 spectra/s] 0.1s | postprocessing 0.0 s 013. CatB_0000_1.raw 10.0 s | deisotoping 0.0 s [progress: 28609/28609 (100%) - 286090 spectra/s] 0.1s | postprocessing 0.0 s 014. CatB_0000_2.raw 9.6 s | deisotoping 0.0 s [progress: 29201/29201 (100%) - 292010 spectra/s] 0.1s | postprocessing 0.0 s 015. CatB_0000_3.raw 10.0 s | deisotoping 0.0 s [progress: 30296/30296 (100%) - 299960 spectra/s] 0.1s | postprocessing 0.0 s 016. CatB_0000_4.raw 10.3 s | deisotoping 0.0 s [progress: 30433/30433 (100%) - 304330 spectra/s] 0.1s | postprocessing 0.0 s 017. CatB_0015_1.raw 10.2 s | deisotoping 0.0 s [progress: 29225/29225 (100%) - 289356 spectra/s] 0.1s | postprocessing 0.0 s 018. CatB_0015_2.raw 10.3 s | deisotoping 0.0 s [progress: 30605/30605 (100%) - 306050 spectra/s] 0.1s | postprocessing 0.0 s 019. CatB_0015_3.raw 10.0 s | deisotoping 0.0 s [progress: 29583/29583 (100%) - 295830 spectra/s] 0.1s | postprocessing 0.0 s 020. CatB_0015_4.raw 10.3 s | deisotoping 0.0 s [progress: 29030/29030 (100%) - 290300 spectra/s] 0.1s | postprocessing 0.0 s 021. CatB_0060_1.raw 9.8 s | deisotoping 0.0 s [progress: 28591/28591 (100%) - 285910 spectra/s] 0.1s | postprocessing 0.0 s 022. CatB_0060_2.raw 9.8 s | deisotoping 0.0 s [progress: 27975/27975 (100%) - 279750 spectra/s] 0.1s | postprocessing 0.0 s 023. CatB_0060_3.raw 9.6 s | deisotoping 0.0 s [progress: 28106/28106 (100%) - 281060 spectra/s] 0.1s | postprocessing 0.0 s 024. CatB_0060_4.raw 9.7 s | deisotoping 0.0 s [progress: 27738/27738 (100%) - 277380 spectra/s] 0.1s | postprocessing 0.0 s 025. CatC_0000_1.raw 9.5 s | deisotoping 0.0 s [progress: 28624/28624 (100%) - 95413 spectra/s] 0.3s | postprocessing 0.0 s 026. CatC_0000_2.raw 7.6 s | deisotoping 0.0 s [progress: 28322/28322 (100%) - 283220 spectra/s] 0.1s | postprocessing 0.0 s 027. CatC_0000_3.raw 9.4 s | deisotoping 0.0 s [progress: 28645/28645 (100%) - 286450 spectra/s] 0.1s | postprocessing 0.0 s 028. CatC_0000_4.raw 9.3 s | deisotoping 0.0 s [progress: 27945/27945 (100%) - 279450 spectra/s] 0.1s | postprocessing 0.0 s 029. CatC_0030_1.raw 9.1 s | deisotoping 0.0 s [progress: 28016/28016 (100%) - 277386 spectra/s] 0.1s | postprocessing 0.0 s 030. CatC_0030_2.raw 9.1 s | deisotoping 0.0 s [progress: 27739/27739 (100%) - 277390 spectra/s] 0.1s | postprocessing 0.0 s 031. CatC_0030_3.raw 9.3 s | deisotoping 0.0 s [progress: 28221/28221 (100%) - 282210 spectra/s] 0.1s | postprocessing 0.0 s 032. CatC_0030_4.raw 9.0 s | deisotoping 0.0 s [progress: 27917/27917 (100%) - 279170 spectra/s] 0.1s | postprocessing 0.0 s 033. CatC_0090_1.raw 9.3 s | deisotoping 0.0 s [progress: 27640/27640 (100%) - 276400 spectra/s] 0.1s | postprocessing 0.0 s 034. CatC_0090_2.raw 9.0 s | deisotoping 0.0 s [progress: 28279/28279 (100%) - 282790 spectra/s] 0.1s | postprocessing 0.0 s 035. CatC_0090_3.raw 9.2 s | deisotoping 0.0 s [progress: 27892/27892 (100%) - 278920 spectra/s] 0.1s | postprocessing 0.0 s 036. CatC_0090_4.raw 9.3 s | deisotoping 0.0 s [progress: 28734/28734 (100%) - 287340 spectra/s] 0.1s | postprocessing 0.0 s 037. CatD_0000_1.raw 7.0 s | deisotoping 0.0 s [progress: 26428/26428 (100%) - 264280 spectra/s] 0.1s | postprocessing 0.0 s 038. CatD_0000_2.raw 7.1 s | deisotoping 0.0 s [progress: 26434/26434 (100%) - 264340 spectra/s] 0.1s | postprocessing 0.0 s 039. CatD_0015_1.raw 6.4 s | deisotoping 0.0 s [progress: 26981/26981 (100%) - 269810 spectra/s] 0.1s | postprocessing 0.0 s 040. CatD_0015_2.raw 6.1 s | deisotoping 0.0 s [progress: 24123/24123 (100%) - 241230 spectra/s] 0.1s | postprocessing 0.0 s 041. CatD_0015_3.raw 6.6 s | deisotoping 0.0 s [progress: 29079/29079 (100%) - 290790 spectra/s] 0.1s | postprocessing 0.0 s 042. CatD_0015_4.raw 6.5 s | deisotoping 0.0 s [progress: 27008/27008 (100%) - 270080 spectra/s] 0.1s | postprocessing 0.0 s ***************************FIRST SEARCH DONE IN 6.291 MIN************************** *********************MASS CALIBRATION AND PARAMETER OPTIMIZATION******************* -----|---------------|---------------|---------------|--------------- | MS1 (Old) | MS1 (New) | MS2 (Old) | MS2 (New) -----|---------------|---------------|---------------|--------------- Run | Median MAD | Median MAD | Median MAD | Median MAD 001 | -2.54 1.92 | -0.35 1.56 | -5.21 2.67 | -0.32 2.47 002 | -2.50 1.79 | -0.44 1.61 | -5.19 2.54 | -0.28 2.37 003 | -2.55 1.67 | -0.35 1.51 | -5.13 2.58 | -0.27 2.42 004 | -2.29 1.74 | -0.37 1.53 | -5.00 2.62 | -0.33 2.46 005 | -2.14 1.80 | -0.40 1.49 | -4.91 2.67 | -0.32 2.48 006 | -2.03 1.88 | -0.33 1.50 | -4.84 2.73 | -0.32 2.48 007 | -2.15 1.92 | -0.44 1.50 | -4.88 2.59 | -0.30 2.40 008 | -2.35 1.81 | -0.42 1.47 | -4.96 2.64 | -0.32 2.48 009 | -2.32 1.76 | -0.56 1.58 | -4.92 2.65 | -0.31 2.47 010 | -2.06 1.90 | -0.37 1.75 | -4.89 2.60 | -0.31 2.40 011 | -2.43 1.71 | -0.58 1.62 | -5.11 2.59 | -0.33 2.38 012 | -2.33 1.94 | -0.54 1.70 | -5.10 2.62 | -0.37 2.43 013 | 2.51 2.37 | -0.42 1.87 | -1.40 2.19 | -0.05 2.12 014 | 2.91 2.07 | -0.39 1.69 | -1.04 2.25 | 0.00 2.20 015 | 2.87 2.31 | -0.18 1.75 | -1.09 2.25 | -0.07 2.18 016 | 2.99 2.32 | -0.36 1.71 | -0.81 2.22 | 0.04 2.15 017 | 3.06 2.31 | -0.25 1.84 | -0.84 2.23 | -0.07 2.18 018 | 2.96 2.32 | -0.32 1.79 | -1.01 2.21 | -0.03 2.19 019 | 2.93 2.22 | -0.35 1.60 | -0.91 2.19 | -0.02 2.17 020 | 2.70 2.26 | -0.39 1.74 | -1.10 2.23 | -0.10 2.18 021 | 2.71 2.30 | -0.20 1.72 | -1.19 2.20 | -0.02 2.09 022 | 3.00 2.18 | -0.24 1.67 | -0.86 2.18 | -0.03 2.11 023 | 3.06 2.27 | -0.21 1.72 | -0.70 2.24 | -0.05 2.20 024 | 3.48 1.97 | -0.29 1.56 | -0.44 2.25 | 0.06 2.22 025 | -2.98 1.95 | -0.32 1.50 | -5.56 2.63 | -0.31 2.44 026 | -2.86 1.90 | -0.44 1.40 | -5.49 2.64 | -0.28 2.46 027 | -3.18 1.86 | -0.25 1.49 | -5.80 2.60 | -0.30 2.41 028 | -3.05 1.92 | -0.26 1.38 | -5.67 2.65 | -0.32 2.46 029 | -2.43 1.84 | -0.26 1.38 | -4.99 2.64 | -0.32 2.44 030 | -2.67 1.83 | -0.30 1.39 | -5.18 2.59 | -0.30 2.38 031 | -2.62 1.81 | -0.25 1.48 | -5.27 2.65 | -0.33 2.47 032 | -2.78 1.85 | -0.32 1.45 | -5.32 2.68 | -0.31 2.45 033 | -2.14 1.81 | -0.20 1.60 | -4.77 2.55 | -0.28 2.40 034 | -2.31 1.76 | -0.36 1.50 | -4.92 2.61 | -0.39 2.42 035 | -2.69 1.79 | -0.37 1.42 | -5.32 2.53 | -0.36 2.37 036 | -2.32 1.82 | -0.33 1.42 | -4.93 2.63 | -0.28 2.45 037 | 4.23 2.09 | -0.38 1.64 | 0.32 2.24 | 0.05 2.19 038 | 4.14 2.08 | -0.25 1.62 | 0.20 2.27 | 0.01 2.23 039 | 4.30 2.17 | -0.35 1.68 | 0.28 2.25 | 0.01 2.21 040 | 4.97 2.59 | -0.23 1.88 | 0.47 2.32 | 0.01 2.29 041 | 4.51 2.17 | -0.40 1.65 | 0.15 2.23 | 0.01 2.18 042 | 3.94 2.02 | -0.41 1.40 | -0.01 2.31 | -0.02 2.26 -----|---------------|---------------|---------------|--------------- Finding the optimal parameters: -------|-------|-------|-------|-------|-------|------- MS2 | 7 | 10 | 15 | 20 | 25 | 30 -------|-------|-------|-------|-------|-------|------- Count | 4482| 4608| 4556| skip rest -------|-------|-------|-------|-------|-------|------- -------|-------|-------|-------|------- Peaks | 300_0 | 200_0 | 150_1 | 100_1 -------|-------|-------|-------|------- Count | 4596| 4595| skip rest -------|-------|-------|-------|------- -------|------- Int. | 1 -------|------- Count | 4493 -------|------- -------|------- Rm P. | 0 -------|------- Count | 4604 -------|------- New fragment_mass_tolerance = 10.000000 PPM New use_topN_peaks = 300 New minimum_ratio = 0.000000 New intensity_transform = 0 New remove_precursor_peak = 0 ************MASS CALIBRATION AND PARAMETER OPTIMIZATION DONE IN 5.132 MIN********* ************************************MAIN SEARCH************************************ Checking database... Parameters: num_threads = 23 database_name = /home/nanopore-catalyst/centralized_files/proteome_databases/2024-09-16-decoys-contam-mspms_peptide_library.fasta.fas decoy_prefix = rev_ precursor_mass_lower = -20.0 precursor_mass_upper = 20.0 precursor_mass_units = 1 data_type = 0 precursor_true_tolerance = 20.0 precursor_true_units = 1 fragment_mass_tolerance = 10.0 fragment_mass_units = 1 calibrate_mass = 2 use_all_mods_in_first_search = 0 write_calibrated_mzml = 0 write_uncalibrated_mgf = 0 write_mzbin_all = 0 isotope_error = 0/1/2 mass_offsets = 0.0 labile_search_mode = OFF restrict_deltamass_to = all precursor_mass_mode = SELECTED localize_delta_mass = 0 delta_mass_exclude_ranges = (-1.5,3.5) fragment_ion_series = b,y ion_series_definitions = search_enzyme_name = stricttrypsin search_enzyme_sense_1 = C search_enzyme_cut_1 = KR search_enzyme_nocut_1 = allowed_missed_cleavage_1 = 2 num_enzyme_termini = 0 clip_nTerm_M = 1 allow_multiple_variable_mods_on_residue = 0 max_variable_mods_per_peptide = 3 max_variable_mods_combinations = 5000 output_format = pepxml_pin output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = 1 override_charge = 0 precursor_charge_low = 1 precursor_charge_high = 4 digest_min_length = 7 digest_max_length = 50 digest_mass_range_low = 500.0 digest_mass_range_high = 5000.0 max_fragment_charge = 1 deisotope = 1 deneutralloss = 1 track_zero_topN = 0 zero_bin_accept_expect = 0.0 zero_bin_mult_expect = 1.0 minimum_peaks = 15 use_topN_peaks = 300 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.0 intensity_transform = 0 activation_types = all group_variable = 0 require_precursor = 1 reuse_dia_fragment_peaks = 0 remove_precursor_peak = 0 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 0.0 clear_mz_range_high = 0.0 excluded_scan_list_file = mass_diff_to_variable_mod = 0 min_sequence_matches = 2 check_spectral_files = 1 add_A_alanine = 0.0 add_B_user_amino_acid = 0.0 add_C_cysteine = 57.02146 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.0 add_E_glutamic_acid = 0.0 add_F_phenylalanine = 0.0 add_G_glycine = 0.0 add_H_histidine = 0.0 add_I_isoleucine = 0.0 add_J_user_amino_acid = 0.0 add_K_lysine = 0.0 add_L_leucine = 0.0 add_M_methionine = 0.0 add_N_asparagine = 0.0 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.0 # O = pyrrolysine (237.14773 Da) add_P_proline = 0.0 add_Q_glutamine = 0.0 add_R_arginine = 0.0 add_S_serine = 0.0 add_T_threonine = 0.0 add_U_user_amino_acid = 0.0 # U = selenocysteine (150.95363 Da) add_V_valine = 0.0 add_W_tryptophan = 0.0 add_X_user_amino_acid = 0.0 add_Y_tyrosine = 0.0 add_Z_user_amino_acid = 0.0 Selected fragment index width 0.05 Da. 129201004 fragments to be searched in 1 slices (1.93 GB total) Operating on slice 1 of 1: Fragment index slice generated in 0.43 s 001. CatA_0000_1.mzBIN_calibrated 0.0 s [progress: 23709/23709 (100%) - 117955 spectra/s] 0.2s | remapping alternative proteins and postprocessing 0.6 s 002. CatA_0000_2.mzBIN_calibrated 0.1 s [progress: 22335/22335 (100%) - 111119 spectra/s] 0.2s | remapping alternative proteins and postprocessing 0.3 s 003. CatA_0000_3.mzBIN_calibrated 0.1 s [progress: 23498/23498 (100%) - 234980 spectra/s] 0.1s | remapping alternative proteins and postprocessing 0.2 s 004. CatA_0000_4.mzBIN_calibrated 0.0 s [progress: 23822/23822 (100%) - 119110 spectra/s] 0.2s | remapping alternative proteins and postprocessing 0.1 s 005. CatA_0030_1.mzBIN_calibrated 0.0 s [progress: 21927/21927 (100%) - 217099 spectra/s] 0.1s | remapping alternative proteins and postprocessing 0.1 s 006. CatA_0030_2.mzBIN_calibrated 0.0 s [progress: 21285/21285 (100%) - 212850 spectra/s] 0.1s | remapping alternative proteins and postprocessing 0.1 s 007. CatA_0030_3.mzBIN_calibrated 0.0 s [progress: 21710/21710 (100%) - 217100 spectra/s] 0.1s | remapping alternative proteins and postprocessing 0.1 s 008. CatA_0030_4.mzBIN_calibrated 0.0 s [progress: 23381/23381 (100%) - 233810 spectra/s] 0.1s | remapping alternative proteins and postprocessing 0.1 s 009. CatA_0090_1.mzBIN_calibrated 0.0 s [progress: 21229/21229 (100%) - 212290 spectra/s] 0.1s | remapping alternative proteins and postprocessing 0.1 s 010. CatA_0090_2.mzBIN_calibrated 0.0 s [progress: 21205/21205 (100%) - 212050 spectra/s] 0.1s | remapping alternative proteins and postprocessing 0.1 s 011. CatA_0090_3.mzBIN_calibrated 0.0 s [progress: 22143/22143 (100%) - 221430 spectra/s] 0.1s | remapping alternative proteins and postprocessing 0.1 s 012. CatA_0090_4.mzBIN_calibrated 0.0 s [progress: 22010/22010 (100%) - 217921 spectra/s] 0.1s | remapping alternative proteins and postprocessing 0.2 s 013. CatB_0000_1.mzBIN_calibrated 0.0 s [progress: 27828/27828 (100%) - 139140 spectra/s] 0.2s | remapping alternative proteins and postprocessing 0.1 s 014. CatB_0000_2.mzBIN_calibrated 0.0 s [progress: 28420/28420 (100%) - 136635 spectra/s] 0.2s | remapping alternative proteins and postprocessing 0.1 s 015. CatB_0000_3.mzBIN_calibrated 0.0 s [progress: 29527/29527 (100%) - 147635 spectra/s] 0.2s | remapping alternative proteins and postprocessing 0.2 s 016. CatB_0000_4.mzBIN_calibrated 0.0 s [progress: 29614/29614 (100%) - 148070 spectra/s] 0.2s | remapping alternative proteins and postprocessing 0.2 s 017. CatB_0015_1.mzBIN_calibrated 0.0 s [progress: 28400/28400 (100%) - 142000 spectra/s] 0.2s | remapping alternative proteins and postprocessing 0.1 s 018. CatB_0015_2.mzBIN_calibrated 0.1 s [progress: 29735/29735 (100%) - 148675 spectra/s] 0.2s | remapping alternative proteins and postprocessing 0.1 s 019. CatB_0015_3.mzBIN_calibrated 0.1 s [progress: 28795/28795 (100%) - 143259 spectra/s] 0.2s | remapping alternative proteins and postprocessing 0.2 s 020. CatB_0015_4.mzBIN_calibrated 0.0 s [progress: 28217/28217 (100%) - 140383 spectra/s] 0.2s | remapping alternative proteins and postprocessing 0.1 s 021. CatB_0060_1.mzBIN_calibrated 0.0 s [progress: 27735/27735 (100%) - 138675 spectra/s] 0.2s | remapping alternative proteins and postprocessing 0.1 s 022. CatB_0060_2.mzBIN_calibrated 0.0 s [progress: 27180/27180 (100%) - 135900 spectra/s] 0.2s | remapping alternative proteins and postprocessing 0.1 s 023. CatB_0060_3.mzBIN_calibrated 0.0 s [progress: 27290/27290 (100%) - 136450 spectra/s] 0.2s | remapping alternative proteins and postprocessing 0.1 s 024. CatB_0060_4.mzBIN_calibrated 0.0 s [progress: 26882/26882 (100%) - 133741 spectra/s] 0.2s | remapping alternative proteins and postprocessing 0.1 s 025. CatC_0000_1.mzBIN_calibrated 0.0 s [progress: 27528/27528 (100%) - 137640 spectra/s] 0.2s | remapping alternative proteins and postprocessing 0.1 s 026. CatC_0000_2.mzBIN_calibrated 0.0 s [progress: 27340/27340 (100%) - 136700 spectra/s] 0.2s | remapping alternative proteins and postprocessing 0.2 s 027. CatC_0000_3.mzBIN_calibrated 0.0 s [progress: 27487/27487 (100%) - 137435 spectra/s] 0.2s | remapping alternative proteins and postprocessing 0.2 s 028. CatC_0000_4.mzBIN_calibrated 0.0 s [progress: 26998/26998 (100%) - 134990 spectra/s] 0.2s | remapping alternative proteins and postprocessing 0.2 s 029. CatC_0030_1.mzBIN_calibrated 0.0 s [progress: 27021/27021 (100%) - 134433 spectra/s] 0.2s | remapping alternative proteins and postprocessing 0.2 s 030. CatC_0030_2.mzBIN_calibrated 0.0 s [progress: 26795/26795 (100%) - 133308 spectra/s] 0.2s | remapping alternative proteins and postprocessing 0.1 s 031. CatC_0030_3.mzBIN_calibrated 0.0 s [progress: 27245/27245 (100%) - 135547 spectra/s] 0.2s | remapping alternative proteins and postprocessing 0.2 s 032. CatC_0030_4.mzBIN_calibrated 0.0 s [progress: 27018/27018 (100%) - 135090 spectra/s] 0.2s | remapping alternative proteins and postprocessing 0.2 s 033. CatC_0090_1.mzBIN_calibrated 0.0 s [progress: 26676/26676 (100%) - 132716 spectra/s] 0.2s | remapping alternative proteins and postprocessing 0.2 s 034. CatC_0090_2.mzBIN_calibrated 0.0 s [progress: 27248/27248 (100%) - 136240 spectra/s] 0.2s | remapping alternative proteins and postprocessing 0.2 s 035. CatC_0090_3.mzBIN_calibrated 0.0 s [progress: 26947/26947 (100%) - 134065 spectra/s] 0.2s | remapping alternative proteins and postprocessing 0.1 s 036. CatC_0090_4.mzBIN_calibrated 0.0 s [progress: 27808/27808 (100%) - 139040 spectra/s] 0.2s | remapping alternative proteins and postprocessing 0.2 s 037. CatD_0000_1.mzBIN_calibrated 0.0 s [progress: 25850/25850 (100%) - 129250 spectra/s] 0.2s | remapping alternative proteins and postprocessing 0.1 s 038. CatD_0000_2.mzBIN_calibrated 0.0 s [progress: 25716/25716 (100%) - 127940 spectra/s] 0.2s | remapping alternative proteins and postprocessing 0.1 s 039. CatD_0015_1.mzBIN_calibrated 0.0 s [progress: 26233/26233 (100%) - 131165 spectra/s] 0.2s | remapping alternative proteins and postprocessing 0.1 s 040. CatD_0015_2.mzBIN_calibrated 0.0 s [progress: 23312/23312 (100%) - 230812 spectra/s] 0.1s | remapping alternative proteins and postprocessing 0.1 s 041. CatD_0015_3.mzBIN_calibrated 0.0 s [progress: 28431/28431 (100%) - 141448 spectra/s] 0.2s | remapping alternative proteins and postprocessing 0.1 s 042. CatD_0015_4.mzBIN_calibrated 0.0 s [progress: 26387/26387 (100%) - 131935 spectra/s] 0.2s | remapping alternative proteins and postprocessing 0.1 s ***************************MAIN SEARCH DONE IN 0.284 MIN*************************** *******************************TOTAL TIME 11.707 MIN******************************** Process 'MSFragger' finished, exit code: 0 MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0000_1.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1/CatA_0000_1.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0000_1.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1/CatA_0000_1.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0000_2.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_2/CatA_0000_2.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0000_2.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_2/CatA_0000_2.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0000_3.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_3/CatA_0000_3.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0000_3.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_3/CatA_0000_3.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0000_4.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_4/CatA_0000_4.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0000_4.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_4/CatA_0000_4.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0030_1.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_1/CatA_0030_1.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0030_1.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_1/CatA_0030_1.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0030_2.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_2/CatA_0030_2.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0030_2.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_2/CatA_0030_2.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0030_3.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_3/CatA_0030_3.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0030_3.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_3/CatA_0030_3.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0030_4.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_4/CatA_0030_4.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0030_4.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_4/CatA_0030_4.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0090_1.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_1/CatA_0090_1.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0090_1.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_1/CatA_0090_1.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0090_2.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_2/CatA_0090_2.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0090_2.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_2/CatA_0090_2.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0090_3.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_3/CatA_0090_3.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0090_3.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_3/CatA_0090_3.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0090_4.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_4/CatA_0090_4.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0090_4.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_4/CatA_0090_4.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0000_1.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_1/CatB_0000_1.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0000_1.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_1/CatB_0000_1.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0000_2.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_2/CatB_0000_2.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0000_2.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_2/CatB_0000_2.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0000_3.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_3/CatB_0000_3.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0000_3.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_3/CatB_0000_3.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0000_4.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_4/CatB_0000_4.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0000_4.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_4/CatB_0000_4.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0015_1.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_1/CatB_0015_1.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0015_1.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_1/CatB_0015_1.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0015_2.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_2/CatB_0015_2.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0015_2.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_2/CatB_0015_2.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0015_3.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_3/CatB_0015_3.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0015_3.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_3/CatB_0015_3.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0015_4.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_4/CatB_0015_4.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0015_4.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_4/CatB_0015_4.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0060_1.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_1/CatB_0060_1.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0060_1.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_1/CatB_0060_1.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0060_2.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_2/CatB_0060_2.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0060_2.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_2/CatB_0060_2.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0060_3.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_3/CatB_0060_3.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0060_3.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_3/CatB_0060_3.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0060_4.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_4/CatB_0060_4.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0060_4.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_4/CatB_0060_4.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0000_1.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_1/CatC_0000_1.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0000_1.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_1/CatC_0000_1.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0000_2.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_2/CatC_0000_2.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0000_2.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_2/CatC_0000_2.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0000_3.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_3/CatC_0000_3.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0000_3.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_3/CatC_0000_3.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0000_4.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_4/CatC_0000_4.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0000_4.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_4/CatC_0000_4.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0030_1.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_1/CatC_0030_1.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0030_1.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_1/CatC_0030_1.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0030_2.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_2/CatC_0030_2.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0030_2.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_2/CatC_0030_2.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0030_3.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_3/CatC_0030_3.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0030_3.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_3/CatC_0030_3.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0030_4.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_4/CatC_0030_4.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0030_4.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_4/CatC_0030_4.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0090_1.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_1/CatC_0090_1.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0090_1.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_1/CatC_0090_1.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0090_2.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_2/CatC_0090_2.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0090_2.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_2/CatC_0090_2.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0090_3.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_3/CatC_0090_3.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0090_3.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_3/CatC_0090_3.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0090_4.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_4/CatC_0090_4.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0090_4.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_4/CatC_0090_4.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0000_1.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0000_1/CatD_0000_1.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0000_1.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0000_1/CatD_0000_1.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0000_2.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0000_2/CatD_0000_2.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0000_2.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0000_2/CatD_0000_2.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0015_1.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_1/CatD_0015_1.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0015_1.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_1/CatD_0015_1.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0015_2.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_2/CatD_0015_2.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0015_2.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_2/CatD_0015_2.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0015_3.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_3/CatD_0015_3.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0015_3.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_3/CatD_0015_3.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0015_4.pepXML /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_4/CatD_0015_4.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar:/home/nanopore-catalyst/fragpipe/lib/commons-io-2.15.1.jar com.github.chhh.utils.FileMove --no-err /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0015_4.pin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_4/CatD_0015_4.pin Process 'MSFragger move pin' finished, exit code: 0 MSBooster [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3] java -Xmx56G -cp /home/nanopore-catalyst/fragpipe/tools/msbooster-1.1.28.jar:/home/nanopore-catalyst/fragpipe/tools/batmass-io-1.30.0.jar Features.MainClass --paramsList /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/msbooster_params.txt MSBooster v1.1.28 Using 23 threads 27436 unique peptides from 259455 PSMs createFull input file generation took 682 milliseconds Input file at /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_2/spectraRT_full.tsv Generating input file for DIA-NN 27436 unique peptides from 259455 PSMs Writing DIA-NN input file Diann input file generation took 518 milliseconds Input file at /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_2/spectraRT.tsv Generating DIA-NN predictions /home/nanopore-catalyst/fragpipe/tools/diann/1.8.2_beta_8/linux/diann-1.8.1.8 --lib /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_2/spectraRT.tsv --predict --threads 23 --strip-unknown-mods --predict-n-frag 100 DIA-NN 1.8.2 beta 8 (Data-Independent Acquisition by Neural Networks) Compiled on Dec 1 2022 14:47:06 Current date and time: Mon Sep 16 18:09:39 2024 Logical CPU cores: 24 Predicted spectra will be saved in a binary format Thread number set to 23 DIA-NN will use deep learning to predict spectra/RTs/IMs even for peptides carrying modifications which are not recognised by the deep learning predictor. In this scenario, if also generating a spectral library from the DIA data or using the MBR mode, it might or might not be better (depends on the data) to also use the --out-measured-rt option - it's recommended to test it with and without this option Deep learning predictor will predict 100 fragments 0 files will be processed [0:00] Loading spectral library /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_2/spectraRT.tsv [0:00] Finding proteotypic peptides (assuming that the list of UniProt ids provided for each peptide is complete) [0:00] Spectral library loaded: 0 protein isoforms, 0 protein groups and 27436 precursors in 24145 elution groups. [0:00] Encoding peptides for spectra and RTs prediction [0:00] Predicting spectra and IMs [0:03] Predicting RTs [0:04] Decoding predicted spectra and IMs [0:04] Decoding RTs [0:04] Saving the list of predictions to /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_2/spectraRT.predicted.bin Finished Done generating DIA-NN predictions Model running took 4975 milliseconds Generating edited pin with following features: [unweightedSpectralEntropy, deltaRTLOESS] Loading predicted spectra Processing /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0000_1_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 459 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1/CatA_0000_1_edited.pin Processing /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0000_2_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 451 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_2/CatA_0000_2_edited.pin Processing /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0000_3_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 440 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_3/CatA_0000_3_edited.pin Processing /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0000_4_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 459 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_4/CatA_0000_4_edited.pin Processing /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0030_1_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 503 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_1/CatA_0030_1_edited.pin Processing /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0030_2_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 470 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_2/CatA_0030_2_edited.pin Processing /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0030_3_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 481 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_3/CatA_0030_3_edited.pin Processing /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0030_4_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 508 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_4/CatA_0030_4_edited.pin Processing /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0090_1_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 497 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_1/CatA_0090_1_edited.pin Processing /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0090_2_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 499 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_2/CatA_0090_2_edited.pin Processing /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0090_3_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 495 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_3/CatA_0090_3_edited.pin Processing /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0090_4_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 466 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_4/CatA_0090_4_edited.pin Processing /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0000_1_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 560 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_1/CatB_0000_1_edited.pin Processing /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0000_2_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 523 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_2/CatB_0000_2_edited.pin Processing /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0000_3_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 581 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_3/CatB_0000_3_edited.pin Processing /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0000_4_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 568 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_4/CatB_0000_4_edited.pin Processing /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0015_1_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 613 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_1/CatB_0015_1_edited.pin Processing /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0015_2_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 557 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_2/CatB_0015_2_edited.pin Processing /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0015_3_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 619 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_3/CatB_0015_3_edited.pin Processing /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0015_4_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 632 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_4/CatB_0015_4_edited.pin Processing /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0060_1_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 630 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_1/CatB_0060_1_edited.pin Processing /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0060_2_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 637 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_2/CatB_0060_2_edited.pin Processing /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0060_3_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 650 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_3/CatB_0060_3_edited.pin Processing /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0060_4_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 610 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_4/CatB_0060_4_edited.pin Processing /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0000_1_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 516 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_1/CatC_0000_1_edited.pin Processing /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0000_2_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 520 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_2/CatC_0000_2_edited.pin Processing /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0000_3_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 515 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_3/CatC_0000_3_edited.pin Processing /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0000_4_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 540 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_4/CatC_0000_4_edited.pin Processing /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0030_1_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 539 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_1/CatC_0030_1_edited.pin Processing /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0030_2_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 542 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_2/CatC_0030_2_edited.pin Processing /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0030_3_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 549 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_3/CatC_0030_3_edited.pin Processing /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0030_4_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 547 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_4/CatC_0030_4_edited.pin Processing /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0090_1_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 551 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_1/CatC_0090_1_edited.pin Processing /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0090_2_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 564 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_2/CatC_0090_2_edited.pin Processing /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0090_3_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 571 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_3/CatC_0090_3_edited.pin Processing /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0090_4_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 561 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_4/CatC_0090_4_edited.pin Processing /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0000_1_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 507 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0000_1/CatD_0000_1_edited.pin Processing /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0000_2_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 495 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0000_2/CatD_0000_2_edited.pin Processing /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0015_1_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 504 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_1/CatD_0015_1_edited.pin Processing /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0015_2_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Not enough high quality PSMs for RT regression with escore cutoff of 3.1622776E-4. Relaxing escore cutoff to 0.01 RT regression using 835 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_2/CatD_0015_2_edited.pin Processing /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0015_3_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 916 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_3/CatD_0015_3_edited.pin Processing /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0015_4_uncalibrated.mzML Loading pin ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% RT regression using 1000 PSMs Calculating features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Writing features ...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Edited pin file at /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_4/CatD_0015_4_edited.pin Feature calculation and edited pin writing done in 45050 ms Process 'MSBooster' finished, exit code: 0 Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_3] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatC_0090_3_percolator_target_psms.tsv --decoy-results-psms CatC_0090_3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatC_0090_3_edited.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 09:42:23 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll (lukall@u.washington.edu) in the Department of Genome Sciences at the University of Washington. Issued command: /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatC_0090_3_percolator_target_psms.tsv --decoy-results-psms CatC_0090_3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatC_0090_3_edited.pin Started Mon Sep 16 18:10:29 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile CatC_0090_3_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other unweighted_spectral_entropy delta_RT_loess Found 7243 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 6338 positives and 905 negatives, size ratio=7.00331 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 28 as initial direction. Could separate 3419 training set positives with q<0.01 in that direction. Split 2: Selected feature 4 as initial direction. Could separate 3307 training set positives with q<0.01 in that direction. Split 3: Selected feature 28 as initial direction. Could separate 3456 training set positives with q<0.01 in that direction. Found 4934 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 2.5758 cpu seconds or 0 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 5391 PSMs with q<0.01 Iteration 2: Estimated 5425 PSMs with q<0.01 Iteration 3: Estimated 5442 PSMs with q<0.01 Iteration 4: Estimated 5446 PSMs with q<0.01 Iteration 5: Estimated 5445 PSMs with q<0.01 Iteration 6: Estimated 5445 PSMs with q<0.01 Iteration 7: Estimated 5445 PSMs with q<0.01 Iteration 8: Estimated 5445 PSMs with q<0.01 Iteration 9: Estimated 5445 PSMs with q<0.01 Iteration 10: Estimated 5445 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName 0.0000 0.0000 0.0000 rank -0.3206 -0.1779 -0.2566 abs_ppm -0.0442 -0.1072 -0.0664 isotope_errors -0.8382 -0.9134 -1.0336 log10_evalue -0.1205 0.1296 -0.4568 hyperscore 0.5202 0.3957 0.4222 delta_hyperscore 0.1178 0.4204 0.2202 matched_ion_num -0.5673 -0.8645 -0.4806 complementary_ions -0.2634 -0.4988 -0.3512 ion_series 0.0516 -0.0280 -0.0707 weighted_average_abs_fragment_ppm -0.0448 -0.0364 0.0968 length_7 0.0771 0.0824 -0.0062 length_8 0.0100 0.0030 -0.0082 length_9_30 -0.0672 -0.0708 -0.1087 length_31 0.0000 0.0000 0.0000 ntt 0.0000 0.0000 0.0000 nmc 0.0000 0.0000 0.0000 charge_1 -0.1537 -0.0509 -0.0700 charge_2 0.1076 0.0213 0.0294 charge_3 0.0366 0.0080 0.0215 charge_4 0.0738 0.1380 0.1396 charge_5 -0.0125 -0.0131 -0.0115 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other 1.2034 0.9420 1.0796 unweighted_spectral_entropy -0.3623 -0.4374 -0.3196 delta_RT_loess 1.0597 1.1171 0.9762 m0 Found 5391 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 6338 target PSMs and 905 decoy PSMs. Calculating q values. Final list yields 5392 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 20.3447 cpu seconds or 9 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_4] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatA_0030_4_percolator_target_psms.tsv --decoy-results-psms CatA_0030_4_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatA_0030_4_edited.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 09:42:23 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll (lukall@u.washington.edu) in the Department of Genome Sciences at the University of Washington. Issued command: /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatA_0030_4_percolator_target_psms.tsv --decoy-results-psms CatA_0030_4_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatA_0030_4_edited.pin Started Mon Sep 16 18:10:38 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile CatA_0030_4_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other unweighted_spectral_entropy delta_RT_loess Found 5606 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 5138 positives and 468 negatives, size ratio=10.9786 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 28 as initial direction. Could separate 2912 training set positives with q<0.01 in that direction. Split 2: Selected feature 28 as initial direction. Could separate 2954 training set positives with q<0.01 in that direction. Split 3: Selected feature 28 as initial direction. Could separate 2919 training set positives with q<0.01 in that direction. Found 4399 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 2.3228 cpu seconds or 1 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 4596 PSMs with q<0.01 Iteration 2: Estimated 4631 PSMs with q<0.01 Iteration 3: Estimated 4633 PSMs with q<0.01 Iteration 4: Estimated 4633 PSMs with q<0.01 Iteration 5: Estimated 4634 PSMs with q<0.01 Iteration 6: Estimated 4633 PSMs with q<0.01 Iteration 7: Estimated 4634 PSMs with q<0.01 Iteration 8: Estimated 4634 PSMs with q<0.01 Iteration 9: Estimated 4634 PSMs with q<0.01 Iteration 10: Estimated 4634 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName 0.0000 0.0000 0.0000 rank -0.1319 -0.1165 -0.1670 abs_ppm -0.0503 -0.1148 -0.1018 isotope_errors -0.8469 -0.9186 -0.6076 log10_evalue -0.1201 0.2300 0.3168 hyperscore 0.4564 -0.1108 0.3004 delta_hyperscore 0.2261 -0.0775 -0.1038 matched_ion_num -0.6630 -0.6557 -0.4740 complementary_ions -0.4758 -0.1150 -0.4410 ion_series -0.0352 -0.0826 -0.0415 weighted_average_abs_fragment_ppm 0.0059 -0.0327 0.1431 length_7 -0.0195 0.0524 -0.0644 length_8 0.0189 -0.0065 -0.0416 length_9_30 -0.0380 -0.0386 -0.0340 length_31 0.0000 0.0000 0.0000 ntt 0.0000 0.0000 0.0000 nmc 0.0000 0.0000 0.0000 charge_1 -0.1439 -0.1344 -0.1797 charge_2 -0.0038 0.0120 0.0404 charge_3 0.1808 0.1294 0.1620 charge_4 0.0281 0.1212 0.0492 charge_5 0.0000 0.0000 0.0000 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other 0.9194 0.8969 1.0243 unweighted_spectral_entropy -0.4972 -0.4941 -0.5148 delta_RT_loess 1.1610 1.1794 1.0384 m0 Found 4600 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 5138 target PSMs and 468 decoy PSMs. Calculating q values. Final list yields 4606 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 33.6011 cpu seconds or 13 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_2] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatC_0030_2_percolator_target_psms.tsv --decoy-results-psms CatC_0030_2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatC_0030_2_edited.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 09:42:23 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll (lukall@u.washington.edu) in the Department of Genome Sciences at the University of Washington. Issued command: /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatC_0030_2_percolator_target_psms.tsv --decoy-results-psms CatC_0030_2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatC_0030_2_edited.pin Started Mon Sep 16 18:10:52 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile CatC_0030_2_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other unweighted_spectral_entropy delta_RT_loess Found 7092 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 6258 positives and 834 negatives, size ratio=7.5036 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 28 as initial direction. Could separate 3347 training set positives with q<0.01 in that direction. Split 2: Selected feature 28 as initial direction. Could separate 3408 training set positives with q<0.01 in that direction. Split 3: Selected feature 28 as initial direction. Could separate 3371 training set positives with q<0.01 in that direction. Found 5039 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 3.1509 cpu seconds or 0 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 5285 PSMs with q<0.01 Iteration 2: Estimated 5321 PSMs with q<0.01 Iteration 3: Estimated 5322 PSMs with q<0.01 Iteration 4: Estimated 5327 PSMs with q<0.01 Iteration 5: Estimated 5322 PSMs with q<0.01 Iteration 6: Estimated 5328 PSMs with q<0.01 Iteration 7: Estimated 5325 PSMs with q<0.01 Iteration 8: Estimated 5330 PSMs with q<0.01 Iteration 9: Estimated 5325 PSMs with q<0.01 Iteration 10: Estimated 5331 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName 0.0000 0.0000 0.0000 rank -0.1740 -0.2706 -0.1828 abs_ppm -0.0921 -0.1245 -0.1316 isotope_errors -1.0505 -0.8085 -1.2255 log10_evalue 0.2008 0.1073 -0.0321 hyperscore 0.3019 0.4668 0.3768 delta_hyperscore -0.1136 0.3589 -0.2234 matched_ion_num -0.6125 -0.6774 -0.5014 complementary_ions -0.3666 -0.4452 -0.3507 ion_series 0.0176 -0.0519 0.0198 weighted_average_abs_fragment_ppm 0.1241 0.0461 0.0844 length_7 -0.0619 0.0200 -0.0422 length_8 -0.0557 -0.0351 0.0106 length_9_30 0.0444 -0.0099 -0.0665 length_31 0.0000 0.0000 0.0000 ntt 0.0000 0.0000 0.0000 nmc 0.0000 0.0000 0.0000 charge_1 -0.0915 -0.0483 -0.1156 charge_2 0.0400 0.0517 0.0652 charge_3 0.0285 -0.0183 0.0452 charge_4 0.1565 0.0426 0.0655 charge_5 -0.0117 -0.0133 -0.0119 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other 1.1289 0.8873 1.0616 unweighted_spectral_entropy -0.4075 -0.3285 -0.3627 delta_RT_loess 0.9824 1.1227 1.0041 m0 Found 5281 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 6258 target PSMs and 834 decoy PSMs. Calculating q values. Final list yields 5303 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 34.7046 cpu seconds or 17 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_1] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatB_0015_1_percolator_target_psms.tsv --decoy-results-psms CatB_0015_1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatB_0015_1_edited.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 09:42:23 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll (lukall@u.washington.edu) in the Department of Genome Sciences at the University of Washington. Issued command: /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatB_0015_1_percolator_target_psms.tsv --decoy-results-psms CatB_0015_1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatB_0015_1_edited.pin Started Mon Sep 16 18:11:09 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile CatB_0015_1_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other unweighted_spectral_entropy delta_RT_loess Found 6660 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 5436 positives and 1224 negatives, size ratio=4.44118 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 28 as initial direction. Could separate 2537 training set positives with q<0.01 in that direction. Split 2: Selected feature 28 as initial direction. Could separate 2457 training set positives with q<0.01 in that direction. Split 3: Selected feature 4 as initial direction. Could separate 2510 training set positives with q<0.01 in that direction. Found 3616 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 3.0391 cpu seconds or 0 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 4008 PSMs with q<0.01 Iteration 2: Estimated 4051 PSMs with q<0.01 Iteration 3: Estimated 4044 PSMs with q<0.01 Iteration 4: Estimated 4047 PSMs with q<0.01 Iteration 5: Estimated 4045 PSMs with q<0.01 Iteration 6: Estimated 4045 PSMs with q<0.01 Iteration 7: Estimated 4044 PSMs with q<0.01 Iteration 8: Estimated 4045 PSMs with q<0.01 Iteration 9: Estimated 4041 PSMs with q<0.01 Iteration 10: Estimated 4043 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName 0.0000 0.0000 0.0000 rank -0.0778 0.0248 -0.0798 abs_ppm 0.0367 -0.0387 -0.1433 isotope_errors -2.0070 -1.3769 -1.1205 log10_evalue -0.8348 0.0403 0.3910 hyperscore 0.8237 0.8895 0.2501 delta_hyperscore 0.8563 0.3622 0.1789 matched_ion_num -0.7880 -0.9361 -0.6132 complementary_ions -1.1483 -1.0858 -0.5376 ion_series -0.1679 -0.1560 -0.0449 weighted_average_abs_fragment_ppm 0.0949 0.0015 -0.0385 length_7 0.0377 0.0636 0.0677 length_8 -0.0308 -0.0445 0.0040 length_9_30 -0.1001 0.0051 -0.0500 length_31 0.0000 0.0000 0.0000 ntt 0.0000 0.0000 0.0000 nmc 0.0000 0.0000 0.0000 charge_1 -0.1346 -0.1769 -0.0532 charge_2 -0.0192 -0.0345 -0.0810 charge_3 0.2013 0.2939 0.2096 charge_4 0.0968 0.0756 -0.0151 charge_5 -0.0112 -0.0094 -0.0123 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other 1.8348 1.8748 1.2843 unweighted_spectral_entropy -0.7397 -0.6850 -0.4285 delta_RT_loess 0.6456 0.5402 0.7083 m0 Found 3990 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 5436 target PSMs and 1224 decoy PSMs. Calculating q values. Final list yields 3990 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 20.3841 cpu seconds or 9 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_4] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatC_0030_4_percolator_target_psms.tsv --decoy-results-psms CatC_0030_4_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatC_0030_4_edited.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 09:42:23 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll (lukall@u.washington.edu) in the Department of Genome Sciences at the University of Washington. Issued command: /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatC_0030_4_percolator_target_psms.tsv --decoy-results-psms CatC_0030_4_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatC_0030_4_edited.pin Started Mon Sep 16 18:11:19 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile CatC_0030_4_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other unweighted_spectral_entropy delta_RT_loess Found 7277 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 6354 positives and 923 negatives, size ratio=6.88407 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 4 as initial direction. Could separate 3356 training set positives with q<0.01 in that direction. Split 2: Selected feature 28 as initial direction. Could separate 3355 training set positives with q<0.01 in that direction. Split 3: Selected feature 28 as initial direction. Could separate 3424 training set positives with q<0.01 in that direction. Found 4918 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 3.0492 cpu seconds or 0 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 5347 PSMs with q<0.01 Iteration 2: Estimated 5385 PSMs with q<0.01 Iteration 3: Estimated 5385 PSMs with q<0.01 Iteration 4: Estimated 5385 PSMs with q<0.01 Iteration 5: Estimated 5386 PSMs with q<0.01 Iteration 6: Estimated 5383 PSMs with q<0.01 Iteration 7: Estimated 5385 PSMs with q<0.01 Iteration 8: Estimated 5383 PSMs with q<0.01 Iteration 9: Estimated 5384 PSMs with q<0.01 Iteration 10: Estimated 5384 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName 0.0000 0.0000 0.0000 rank -0.1237 -0.1617 -0.1579 abs_ppm -0.1262 -0.0849 0.0112 isotope_errors -0.9852 -1.5538 -1.1473 log10_evalue 0.0770 0.6032 0.2271 hyperscore 0.3482 0.2749 0.3335 delta_hyperscore 0.4042 -0.4469 0.4126 matched_ion_num -0.7741 -0.8055 -0.9590 complementary_ions -0.4191 -0.6405 -0.7708 ion_series -0.0712 -0.1200 -0.0823 weighted_average_abs_fragment_ppm -0.0085 -0.0095 -0.0236 length_7 -0.0023 -0.0205 0.0983 length_8 0.0387 0.0552 -0.0277 length_9_30 -0.0701 -0.0791 -0.0475 length_31 0.0000 0.0000 0.0000 ntt 0.0000 0.0000 0.0000 nmc 0.0000 0.0000 0.0000 charge_1 -0.1185 -0.1731 -0.1204 charge_2 0.0067 0.0806 0.0534 charge_3 0.1241 0.0529 0.0465 charge_4 0.0901 0.2608 0.1546 charge_5 -0.0198 -0.0223 -0.0134 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other 1.1233 1.6623 1.1326 unweighted_spectral_entropy -0.3508 -0.6030 -0.3497 delta_RT_loess 1.1947 1.3466 0.8082 m0 Found 5352 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 6354 target PSMs and 923 decoy PSMs. Calculating q values. Final list yields 5359 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 15.4515 cpu seconds or 5 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_2] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatA_0000_2_percolator_target_psms.tsv --decoy-results-psms CatA_0000_2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatA_0000_2_edited.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 09:42:23 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll (lukall@u.washington.edu) in the Department of Genome Sciences at the University of Washington. Issued command: /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatA_0000_2_percolator_target_psms.tsv --decoy-results-psms CatA_0000_2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatA_0000_2_edited.pin Started Mon Sep 16 18:11:24 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile CatA_0000_2_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other unweighted_spectral_entropy delta_RT_loess Found 5099 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 4642 positives and 457 negatives, size ratio=10.1575 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 28 as initial direction. Could separate 2653 training set positives with q<0.01 in that direction. Split 2: Selected feature 28 as initial direction. Could separate 2617 training set positives with q<0.01 in that direction. Split 3: Selected feature 28 as initial direction. Could separate 2642 training set positives with q<0.01 in that direction. Found 3940 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 2.5444 cpu seconds or 0 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 4156 PSMs with q<0.01 Iteration 2: Estimated 4194 PSMs with q<0.01 Iteration 3: Estimated 4196 PSMs with q<0.01 Iteration 4: Estimated 4196 PSMs with q<0.01 Iteration 5: Estimated 4197 PSMs with q<0.01 Iteration 6: Estimated 4196 PSMs with q<0.01 Iteration 7: Estimated 4199 PSMs with q<0.01 Iteration 8: Estimated 4200 PSMs with q<0.01 Iteration 9: Estimated 4200 PSMs with q<0.01 Iteration 10: Estimated 4200 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName 0.0000 0.0000 0.0000 rank -0.2217 -0.1431 -0.1933 abs_ppm -0.0781 -0.1849 -0.1011 isotope_errors -0.9157 -1.1120 -1.0081 log10_evalue -0.0722 0.1323 -0.4383 hyperscore 0.2041 -0.0738 0.0901 delta_hyperscore -0.1906 0.0221 -0.0086 matched_ion_num -0.5155 -0.6104 -0.2353 complementary_ions -0.3060 -0.5116 -0.2930 ion_series -0.0883 -0.2658 -0.2345 weighted_average_abs_fragment_ppm -0.0225 -0.0582 0.2231 length_7 -0.0393 0.0903 -0.1427 length_8 0.0531 -0.0140 -0.0542 length_9_30 -0.0388 -0.0397 0.0228 length_31 0.0000 0.0000 0.0000 ntt 0.0000 0.0000 0.0000 nmc 0.0000 0.0000 0.0000 charge_1 -0.0980 -0.0983 -0.1320 charge_2 -0.0052 0.0332 0.0317 charge_3 0.1164 0.0583 0.1063 charge_4 0.0524 0.0849 0.0636 charge_5 -0.0147 -0.0150 -0.0164 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other 1.0305 1.0186 0.9505 unweighted_spectral_entropy -0.4036 -0.4294 -0.4952 delta_RT_loess 1.0469 1.0714 1.1678 m0 Found 4173 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 4642 target PSMs and 457 decoy PSMs. Calculating q values. Final list yields 4175 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 33.3488 cpu seconds or 21 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_1] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatC_0090_1_percolator_target_psms.tsv --decoy-results-psms CatC_0090_1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatC_0090_1_edited.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 09:42:23 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll (lukall@u.washington.edu) in the Department of Genome Sciences at the University of Washington. Issued command: /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatC_0090_1_percolator_target_psms.tsv --decoy-results-psms CatC_0090_1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatC_0090_1_edited.pin Started Mon Sep 16 18:11:45 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile CatC_0090_1_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other unweighted_spectral_entropy delta_RT_loess Found 7037 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 6155 positives and 882 negatives, size ratio=6.97846 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 4 as initial direction. Could separate 3256 training set positives with q<0.01 in that direction. Split 2: Selected feature 28 as initial direction. Could separate 3311 training set positives with q<0.01 in that direction. Split 3: Selected feature 28 as initial direction. Could separate 3250 training set positives with q<0.01 in that direction. Found 4754 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 2.8371 cpu seconds or 0 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 5164 PSMs with q<0.01 Iteration 2: Estimated 5207 PSMs with q<0.01 Iteration 3: Estimated 5215 PSMs with q<0.01 Iteration 4: Estimated 5218 PSMs with q<0.01 Iteration 5: Estimated 5219 PSMs with q<0.01 Iteration 6: Estimated 5219 PSMs with q<0.01 Iteration 7: Estimated 5219 PSMs with q<0.01 Iteration 8: Estimated 5219 PSMs with q<0.01 Iteration 9: Estimated 5219 PSMs with q<0.01 Iteration 10: Estimated 5219 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName 0.0000 0.0000 0.0000 rank -0.2920 -0.2657 -0.2227 abs_ppm 0.0016 -0.0016 -0.0209 isotope_errors -0.8363 -1.0584 -0.9770 log10_evalue 0.2803 -0.1634 -0.1143 hyperscore 0.6158 0.2259 0.5293 delta_hyperscore -0.0519 0.2756 -0.0677 matched_ion_num -0.6038 -0.6546 -0.5048 complementary_ions -0.3185 -0.5050 -0.4651 ion_series 0.0201 -0.1035 -0.0357 weighted_average_abs_fragment_ppm -0.0099 -0.0133 -0.0140 length_7 -0.0013 -0.0346 0.0178 length_8 0.0302 0.0507 0.0160 length_9_30 -0.0572 -0.0486 -0.0459 length_31 0.0000 0.0000 0.0000 ntt 0.0000 0.0000 0.0000 nmc 0.0000 0.0000 0.0000 charge_1 -0.1431 -0.0780 -0.1590 charge_2 0.0542 0.0352 0.0028 charge_3 0.1024 0.0492 0.1767 charge_4 0.0483 0.0222 0.1377 charge_5 -0.0185 -0.0157 -0.0149 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other 1.0542 1.2020 1.2541 unweighted_spectral_entropy -0.4431 -0.4154 -0.4498 delta_RT_loess 1.0986 0.9340 0.8813 m0 Found 5181 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 6155 target PSMs and 882 decoy PSMs. Calculating q values. Final list yields 5183 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 23.5346 cpu seconds or 10 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_1] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatB_0060_1_percolator_target_psms.tsv --decoy-results-psms CatB_0060_1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatB_0060_1_edited.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 09:42:23 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll (lukall@u.washington.edu) in the Department of Genome Sciences at the University of Washington. Issued command: /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatB_0060_1_percolator_target_psms.tsv --decoy-results-psms CatB_0060_1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatB_0060_1_edited.pin Started Mon Sep 16 18:11:55 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile CatB_0060_1_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other unweighted_spectral_entropy delta_RT_loess Found 6441 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 5305 positives and 1136 negatives, size ratio=4.66989 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 28 as initial direction. Could separate 2520 training set positives with q<0.01 in that direction. Split 2: Selected feature 28 as initial direction. Could separate 2539 training set positives with q<0.01 in that direction. Split 3: Selected feature 28 as initial direction. Could separate 2602 training set positives with q<0.01 in that direction. Found 3791 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 2.6633 cpu seconds or 0 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 4093 PSMs with q<0.01 Iteration 2: Estimated 4142 PSMs with q<0.01 Iteration 3: Estimated 4152 PSMs with q<0.01 Iteration 4: Estimated 4159 PSMs with q<0.01 Iteration 5: Estimated 4162 PSMs with q<0.01 Iteration 6: Estimated 4165 PSMs with q<0.01 Iteration 7: Estimated 4166 PSMs with q<0.01 Iteration 8: Estimated 4167 PSMs with q<0.01 Iteration 9: Estimated 4170 PSMs with q<0.01 Iteration 10: Estimated 4170 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName 0.0000 0.0000 0.0000 rank 0.0695 -0.0317 -0.0636 abs_ppm -0.1527 -0.1145 -0.0564 isotope_errors -1.1238 -1.3956 -1.2644 log10_evalue -0.0552 -0.5056 -1.1518 hyperscore 0.9307 0.7008 0.9085 delta_hyperscore 0.7465 0.3341 1.5337 matched_ion_num -1.0375 -0.6002 -0.7876 complementary_ions -1.0328 -0.1612 -0.9177 ion_series -0.1615 -0.0602 -0.1156 weighted_average_abs_fragment_ppm -0.0286 -0.0236 -0.0200 length_7 0.1161 0.1094 0.1256 length_8 -0.0419 -0.0322 -0.0512 length_9_30 -0.0527 -0.0723 -0.0589 length_31 0.0000 0.0000 0.0000 ntt 0.0000 0.0000 0.0000 nmc 0.0000 0.0000 0.0000 charge_1 -0.1728 -0.1891 -0.1144 charge_2 0.1153 0.0562 0.0334 charge_3 0.0666 0.2173 0.1379 charge_4 0.0317 -0.0969 -0.0782 charge_5 -0.0112 -0.0154 -0.0125 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other 1.8193 1.6891 1.6424 unweighted_spectral_entropy -0.7646 -1.0858 -0.6008 delta_RT_loess 0.8998 1.2349 1.0059 m0 Found 4091 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 5305 target PSMs and 1136 decoy PSMs. Calculating q values. Final list yields 4091 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 16.4295 cpu seconds or 5 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_1] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatD_0015_1_percolator_target_psms.tsv --decoy-results-psms CatD_0015_1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatD_0015_1_edited.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 09:42:23 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll (lukall@u.washington.edu) in the Department of Genome Sciences at the University of Washington. Issued command: /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatD_0015_1_percolator_target_psms.tsv --decoy-results-psms CatD_0015_1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatD_0015_1_edited.pin Started Mon Sep 16 18:12:00 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile CatD_0015_1_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other unweighted_spectral_entropy delta_RT_loess Found 5187 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 4381 positives and 806 negatives, size ratio=5.43548 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 28 as initial direction. Could separate 2207 training set positives with q<0.01 in that direction. Split 2: Selected feature 28 as initial direction. Could separate 2142 training set positives with q<0.01 in that direction. Split 3: Selected feature 28 as initial direction. Could separate 2183 training set positives with q<0.01 in that direction. Found 3205 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 2.3710 cpu seconds or 0 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 3491 PSMs with q<0.01 Iteration 2: Estimated 3521 PSMs with q<0.01 Iteration 3: Estimated 3523 PSMs with q<0.01 Iteration 4: Estimated 3521 PSMs with q<0.01 Iteration 5: Estimated 3529 PSMs with q<0.01 Iteration 6: Estimated 3528 PSMs with q<0.01 Iteration 7: Estimated 3528 PSMs with q<0.01 Iteration 8: Estimated 3528 PSMs with q<0.01 Iteration 9: Estimated 3528 PSMs with q<0.01 Iteration 10: Estimated 3528 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName 0.0000 0.0000 0.0000 rank -0.0174 -0.1675 -0.1916 abs_ppm 0.0852 -0.0426 -0.0633 isotope_errors -2.8589 -1.0892 -1.0269 log10_evalue -1.3083 -0.0043 -0.1662 hyperscore 0.2243 0.3391 0.3776 delta_hyperscore 0.2958 -0.1892 -0.0760 matched_ion_num -0.8834 -0.6368 -0.4735 complementary_ions -0.6084 -0.0780 -0.3814 ion_series -0.1380 -0.0473 -0.0564 weighted_average_abs_fragment_ppm 0.0320 0.0130 0.0117 length_7 -0.0369 -0.0288 -0.0056 length_8 0.0251 0.0286 0.0121 length_9_30 -0.0690 -0.0566 -0.0517 length_31 0.0000 0.0000 0.0000 ntt 0.0000 0.0000 0.0000 nmc 0.0000 0.0000 0.0000 charge_1 -0.2269 -0.1722 -0.2098 charge_2 0.0722 -0.0220 0.0801 charge_3 0.2099 0.2776 0.1757 charge_4 0.0142 -0.0141 0.0072 charge_5 -0.0203 -0.0167 -0.0152 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other 1.7406 1.3575 1.5686 unweighted_spectral_entropy -0.6741 -0.5430 -0.5523 delta_RT_loess 1.0339 0.8487 0.7752 m0 Found 3487 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 4381 target PSMs and 806 decoy PSMs. Calculating q values. Final list yields 3497 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 19.8998 cpu seconds or 9 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_1] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatA_0030_1_percolator_target_psms.tsv --decoy-results-psms CatA_0030_1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatA_0030_1_edited.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 09:42:23 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll (lukall@u.washington.edu) in the Department of Genome Sciences at the University of Washington. Issued command: /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatA_0030_1_percolator_target_psms.tsv --decoy-results-psms CatA_0030_1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatA_0030_1_edited.pin Started Mon Sep 16 18:12:09 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile CatA_0030_1_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other unweighted_spectral_entropy delta_RT_loess Found 4994 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 4601 positives and 393 negatives, size ratio=11.7074 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 28 as initial direction. Could separate 2673 training set positives with q<0.01 in that direction. Split 2: Selected feature 28 as initial direction. Could separate 2637 training set positives with q<0.01 in that direction. Split 3: Selected feature 28 as initial direction. Could separate 2658 training set positives with q<0.01 in that direction. Found 3966 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 2.2619 cpu seconds or 0 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 4141 PSMs with q<0.01 Iteration 2: Estimated 4152 PSMs with q<0.01 Iteration 3: Estimated 4157 PSMs with q<0.01 Iteration 4: Estimated 4158 PSMs with q<0.01 Iteration 5: Estimated 4160 PSMs with q<0.01 Iteration 6: Estimated 4160 PSMs with q<0.01 Iteration 7: Estimated 4162 PSMs with q<0.01 Iteration 8: Estimated 4162 PSMs with q<0.01 Iteration 9: Estimated 4162 PSMs with q<0.01 Iteration 10: Estimated 4162 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName 0.0000 0.0000 0.0000 rank -0.2904 -0.2143 -0.2600 abs_ppm -0.0703 0.1225 -0.0151 isotope_errors -0.7794 -1.3289 -0.7196 log10_evalue 0.2190 -0.3273 0.2838 hyperscore 0.0633 0.5806 0.3830 delta_hyperscore 0.0146 -0.6681 -0.6255 matched_ion_num -0.7057 -0.2723 -0.3204 complementary_ions 0.1005 -0.2280 -0.3339 ion_series -0.0063 -0.0133 0.0807 weighted_average_abs_fragment_ppm 0.0728 0.0157 -0.0620 length_7 -0.0039 0.0372 0.1029 length_8 -0.0416 -0.0341 -0.0231 length_9_30 -0.0361 -0.0158 -0.0301 length_31 0.0000 0.0000 0.0000 ntt 0.0000 0.0000 0.0000 nmc 0.0000 0.0000 0.0000 charge_1 -0.0643 -0.1037 -0.1319 charge_2 0.0595 0.0885 0.1480 charge_3 -0.0391 -0.0232 -0.0477 charge_4 0.2023 0.1732 0.0631 charge_5 0.0000 0.0000 0.0000 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other 0.8127 0.9247 1.2576 unweighted_spectral_entropy -0.4324 -0.6627 -0.5772 delta_RT_loess 1.4734 0.6431 1.2283 m0 Found 4153 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 4601 target PSMs and 393 decoy PSMs. Calculating q values. Final list yields 4159 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 33.7177 cpu seconds or 16 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_3] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatB_0000_3_percolator_target_psms.tsv --decoy-results-psms CatB_0000_3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatB_0000_3_edited.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 09:42:23 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll (lukall@u.washington.edu) in the Department of Genome Sciences at the University of Washington. Issued command: /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatB_0000_3_percolator_target_psms.tsv --decoy-results-psms CatB_0000_3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatB_0000_3_edited.pin Started Mon Sep 16 18:12:25 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile CatB_0000_3_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other unweighted_spectral_entropy delta_RT_loess Found 7371 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 5821 positives and 1550 negatives, size ratio=3.75548 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 28 as initial direction. Could separate 2568 training set positives with q<0.01 in that direction. Split 2: Selected feature 28 as initial direction. Could separate 2603 training set positives with q<0.01 in that direction. Split 3: Selected feature 28 as initial direction. Could separate 2576 training set positives with q<0.01 in that direction. Found 3841 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 3.7275 cpu seconds or 0 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 4124 PSMs with q<0.01 Iteration 2: Estimated 4162 PSMs with q<0.01 Iteration 3: Estimated 4180 PSMs with q<0.01 Iteration 4: Estimated 4175 PSMs with q<0.01 Iteration 5: Estimated 4167 PSMs with q<0.01 Iteration 6: Estimated 4164 PSMs with q<0.01 Iteration 7: Estimated 4163 PSMs with q<0.01 Iteration 8: Estimated 4166 PSMs with q<0.01 Iteration 9: Estimated 4165 PSMs with q<0.01 Iteration 10: Estimated 4163 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName 0.0000 0.0000 0.0000 rank -0.1071 -0.0559 -0.0803 abs_ppm -0.1460 -0.1861 -0.0727 isotope_errors -1.1662 -1.0443 -1.7715 log10_evalue 0.1107 0.1610 -0.7345 hyperscore 0.5941 0.3032 0.3038 delta_hyperscore 0.4338 0.2149 0.8028 matched_ion_num -0.6482 -0.6306 -0.8354 complementary_ions -0.1596 -0.2484 -0.4510 ion_series -0.0533 -0.0601 -0.0469 weighted_average_abs_fragment_ppm -0.0251 -0.0549 0.0010 length_7 -0.0744 0.0529 -0.0544 length_8 0.0926 0.0184 0.0504 length_9_30 -0.0584 -0.0365 -0.0314 length_31 0.0000 0.0000 0.0000 ntt 0.0000 0.0000 0.0000 nmc 0.0000 0.0000 0.0000 charge_1 -0.0162 -0.0463 -0.0449 charge_2 -0.0087 -0.0245 -0.0014 charge_3 0.0314 0.0994 0.0564 charge_4 0.0208 0.0259 0.0419 charge_5 0.0000 0.0000 0.0000 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other 1.3415 1.3603 1.4584 unweighted_spectral_entropy -0.6115 -0.1833 -0.2601 delta_RT_loess 0.8006 0.4998 0.4307 m0 Found 4085 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 5821 target PSMs and 1550 decoy PSMs. Calculating q values. Final list yields 4087 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 22.9703 cpu seconds or 12 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_2] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatA_0090_2_percolator_target_psms.tsv --decoy-results-psms CatA_0090_2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatA_0090_2_edited.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 09:42:23 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll (lukall@u.washington.edu) in the Department of Genome Sciences at the University of Washington. Issued command: /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatA_0090_2_percolator_target_psms.tsv --decoy-results-psms CatA_0090_2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatA_0090_2_edited.pin Started Mon Sep 16 18:12:37 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile CatA_0090_2_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other unweighted_spectral_entropy delta_RT_loess Found 4980 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 4575 positives and 405 negatives, size ratio=11.2963 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 28 as initial direction. Could separate 2680 training set positives with q<0.01 in that direction. Split 2: Selected feature 28 as initial direction. Could separate 2618 training set positives with q<0.01 in that direction. Split 3: Selected feature 28 as initial direction. Could separate 2635 training set positives with q<0.01 in that direction. Found 3955 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 2.3014 cpu seconds or 0 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 4150 PSMs with q<0.01 Iteration 2: Estimated 4168 PSMs with q<0.01 Iteration 3: Estimated 4172 PSMs with q<0.01 Iteration 4: Estimated 4174 PSMs with q<0.01 Iteration 5: Estimated 4174 PSMs with q<0.01 Iteration 6: Estimated 4173 PSMs with q<0.01 Iteration 7: Estimated 4172 PSMs with q<0.01 Iteration 8: Estimated 4173 PSMs with q<0.01 Iteration 9: Estimated 4173 PSMs with q<0.01 Iteration 10: Estimated 4173 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName 0.0000 0.0000 0.0000 rank -0.0621 -0.0334 -0.1229 abs_ppm -0.0983 -0.1800 -0.1179 isotope_errors -0.9968 -1.2888 -0.8291 log10_evalue 0.2348 -0.0319 0.4542 hyperscore 0.1660 0.1783 0.2713 delta_hyperscore -0.1136 -0.1378 -0.1218 matched_ion_num -0.7717 -0.8246 -0.7923 complementary_ions -0.4382 -0.3041 -0.1205 ion_series -0.0409 0.0057 0.0506 weighted_average_abs_fragment_ppm 0.0254 0.0233 -0.0113 length_7 -0.0229 0.0229 -0.0140 length_8 0.0012 -0.0278 0.0235 length_9_30 -0.0265 -0.0264 -0.0345 length_31 0.0000 0.0000 0.0000 ntt 0.0000 0.0000 0.0000 nmc 0.0000 0.0000 0.0000 charge_1 -0.1464 -0.1554 -0.1153 charge_2 0.0164 0.0434 -0.0087 charge_3 0.1585 0.1287 0.1511 charge_4 0.0178 0.0450 0.0312 charge_5 0.0000 0.0000 0.0000 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other 0.8178 0.8462 0.7568 unweighted_spectral_entropy -0.4562 -0.5601 -0.3886 delta_RT_loess 1.0783 1.0770 1.4066 m0 Found 4169 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 4575 target PSMs and 405 decoy PSMs. Calculating q values. Final list yields 4177 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 27.4629 cpu seconds or 6 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_3] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatB_0060_3_percolator_target_psms.tsv --decoy-results-psms CatB_0060_3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatB_0060_3_edited.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 09:42:23 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll (lukall@u.washington.edu) in the Department of Genome Sciences at the University of Washington. Issued command: /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatB_0060_3_percolator_target_psms.tsv --decoy-results-psms CatB_0060_3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatB_0060_3_edited.pin Started Mon Sep 16 18:12:43 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile CatB_0060_3_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other unweighted_spectral_entropy delta_RT_loess Found 6515 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 5443 positives and 1072 negatives, size ratio=5.07743 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 28 as initial direction. Could separate 2740 training set positives with q<0.01 in that direction. Split 2: Selected feature 28 as initial direction. Could separate 2641 training set positives with q<0.01 in that direction. Split 3: Selected feature 28 as initial direction. Could separate 2744 training set positives with q<0.01 in that direction. Found 4026 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 2.6986 cpu seconds or 0 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 4250 PSMs with q<0.01 Iteration 2: Estimated 4289 PSMs with q<0.01 Iteration 3: Estimated 4290 PSMs with q<0.01 Iteration 4: Estimated 4290 PSMs with q<0.01 Iteration 5: Estimated 4292 PSMs with q<0.01 Iteration 6: Estimated 4291 PSMs with q<0.01 Iteration 7: Estimated 4290 PSMs with q<0.01 Iteration 8: Estimated 4290 PSMs with q<0.01 Iteration 9: Estimated 4290 PSMs with q<0.01 Iteration 10: Estimated 4290 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName 0.0000 0.0000 0.0000 rank -0.1838 -0.1573 -0.1716 abs_ppm -0.0122 -0.0310 0.0650 isotope_errors -1.1609 -0.9473 -0.9427 log10_evalue -0.3265 -0.1298 0.1403 hyperscore 0.4112 0.5951 0.4499 delta_hyperscore 0.0746 -0.0183 -0.0376 matched_ion_num -0.5482 -0.5614 -0.4993 complementary_ions 0.0963 -0.1616 -0.3066 ion_series -0.0566 -0.0123 0.0083 weighted_average_abs_fragment_ppm 0.2595 0.2952 0.0396 length_7 -0.0434 -0.0665 0.0400 length_8 -0.1107 -0.1373 -0.0517 length_9_30 -0.0568 -0.0048 -0.0014 length_31 0.0000 0.0000 0.0000 ntt 0.0000 0.0000 0.0000 nmc 0.0000 0.0000 0.0000 charge_1 -0.0647 -0.0319 -0.0827 charge_2 0.0708 0.0418 0.0263 charge_3 -0.0177 -0.0265 0.0733 charge_4 0.0189 0.0447 0.0278 charge_5 0.0000 0.0000 0.0000 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other 1.1116 1.1432 1.1478 unweighted_spectral_entropy -0.5432 -0.4934 -0.4370 delta_RT_loess 0.9751 0.6379 0.7314 m0 Found 4283 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 5443 target PSMs and 1072 decoy PSMs. Calculating q values. Final list yields 4284 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 14.0133 cpu seconds or 4 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_4] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatD_0015_4_percolator_target_psms.tsv --decoy-results-psms CatD_0015_4_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatD_0015_4_edited.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 09:42:23 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll (lukall@u.washington.edu) in the Department of Genome Sciences at the University of Washington. Issued command: /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatD_0015_4_percolator_target_psms.tsv --decoy-results-psms CatD_0015_4_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatD_0015_4_edited.pin Started Mon Sep 16 18:12:47 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile CatD_0015_4_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other unweighted_spectral_entropy delta_RT_loess Found 6040 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 5003 positives and 1037 negatives, size ratio=4.82449 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 28 as initial direction. Could separate 2410 training set positives with q<0.01 in that direction. Split 2: Selected feature 28 as initial direction. Could separate 2399 training set positives with q<0.01 in that direction. Split 3: Selected feature 28 as initial direction. Could separate 2335 training set positives with q<0.01 in that direction. Found 3500 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 2.2984 cpu seconds or 0 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 3846 PSMs with q<0.01 Iteration 2: Estimated 3882 PSMs with q<0.01 Iteration 3: Estimated 3885 PSMs with q<0.01 Iteration 4: Estimated 3882 PSMs with q<0.01 Iteration 5: Estimated 3881 PSMs with q<0.01 Iteration 6: Estimated 3890 PSMs with q<0.01 Iteration 7: Estimated 3885 PSMs with q<0.01 Iteration 8: Estimated 3888 PSMs with q<0.01 Iteration 9: Estimated 3888 PSMs with q<0.01 Iteration 10: Estimated 3889 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName 0.0000 0.0000 0.0000 rank -0.1622 -0.4377 -0.3067 abs_ppm 0.0438 -0.0335 -0.1037 isotope_errors -1.3616 -1.6497 -1.6143 log10_evalue -0.4599 -0.7650 -0.5678 hyperscore 0.6715 0.7127 0.8425 delta_hyperscore -0.0129 0.0585 0.7149 matched_ion_num -0.5529 -0.7247 -0.5972 complementary_ions -0.0399 -0.3233 -0.4287 ion_series -0.0778 -0.0796 -0.0212 weighted_average_abs_fragment_ppm 0.2520 0.0141 -0.0145 length_7 -0.0835 -0.0441 0.0911 length_8 -0.0924 0.0403 -0.0245 length_9_30 -0.0563 -0.0593 -0.0880 length_31 0.0000 0.0000 0.0000 ntt 0.0000 0.0000 0.0000 nmc 0.0000 0.0000 0.0000 charge_1 -0.0827 -0.1800 -0.1110 charge_2 -0.0165 0.0101 -0.0498 charge_3 0.1098 0.2413 0.2196 charge_4 0.0945 -0.0645 -0.0067 charge_5 -0.0090 -0.0118 -0.0176 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other 1.3891 1.9997 1.5586 unweighted_spectral_entropy -0.6462 -0.9012 -0.6849 delta_RT_loess 0.7017 0.9202 1.3647 m0 Found 3830 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 5003 target PSMs and 1037 decoy PSMs. Calculating q values. Final list yields 3849 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 18.5921 cpu seconds or 10 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_2] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatA_0030_2_percolator_target_psms.tsv --decoy-results-psms CatA_0030_2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatA_0030_2_edited.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 09:42:23 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll (lukall@u.washington.edu) in the Department of Genome Sciences at the University of Washington. Issued command: /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatA_0030_2_percolator_target_psms.tsv --decoy-results-psms CatA_0030_2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatA_0030_2_edited.pin Started Mon Sep 16 18:12:57 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile CatA_0030_2_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other unweighted_spectral_entropy delta_RT_loess Found 4786 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 4416 positives and 370 negatives, size ratio=11.9351 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 28 as initial direction. Could separate 2537 training set positives with q<0.01 in that direction. Split 2: Selected feature 28 as initial direction. Could separate 2543 training set positives with q<0.01 in that direction. Split 3: Selected feature 28 as initial direction. Could separate 2585 training set positives with q<0.01 in that direction. Found 3816 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 2.1973 cpu seconds or 0 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 3988 PSMs with q<0.01 Iteration 2: Estimated 4004 PSMs with q<0.01 Iteration 3: Estimated 4011 PSMs with q<0.01 Iteration 4: Estimated 4014 PSMs with q<0.01 Iteration 5: Estimated 4014 PSMs with q<0.01 Iteration 6: Estimated 4014 PSMs with q<0.01 Iteration 7: Estimated 4014 PSMs with q<0.01 Iteration 8: Estimated 4014 PSMs with q<0.01 Iteration 9: Estimated 4014 PSMs with q<0.01 Iteration 10: Estimated 4014 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName 0.0000 0.0000 0.0000 rank -0.3350 -0.1655 -0.3408 abs_ppm -0.0283 0.0108 -0.0416 isotope_errors -0.5061 -0.8321 -1.0289 log10_evalue 0.4220 0.6820 -0.7196 hyperscore 0.2956 0.2639 0.0088 delta_hyperscore -0.2182 -0.6238 0.5654 matched_ion_num -0.6868 -0.3842 -0.7103 complementary_ions -0.0893 -0.5897 -0.1435 ion_series -0.1241 -0.1528 -0.1716 weighted_average_abs_fragment_ppm -0.0360 -0.0038 -0.0366 length_7 0.0176 0.1536 0.0453 length_8 0.0156 -0.1067 -0.0037 length_9_30 -0.0250 -0.0102 -0.0268 length_31 0.0000 0.0000 0.0000 ntt 0.0000 0.0000 0.0000 nmc 0.0000 0.0000 0.0000 charge_1 -0.1562 -0.2262 -0.2007 charge_2 0.0031 0.0340 0.1461 charge_3 0.1864 0.2179 0.0429 charge_4 0.0281 0.1058 0.0541 charge_5 0.0000 0.0000 0.0000 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other 0.9053 1.0526 1.1001 unweighted_spectral_entropy -0.5646 -0.7756 -0.5984 delta_RT_loess 1.2242 0.4989 1.3128 m0 Found 3987 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 4416 target PSMs and 370 decoy PSMs. Calculating q values. Final list yields 3988 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 33.6820 cpu seconds or 14 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_2] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatD_0015_2_percolator_target_psms.tsv --decoy-results-psms CatD_0015_2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatD_0015_2_edited.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 09:42:23 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll (lukall@u.washington.edu) in the Department of Genome Sciences at the University of Washington. Issued command: /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatD_0015_2_percolator_target_psms.tsv --decoy-results-psms CatD_0015_2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatD_0015_2_edited.pin Started Mon Sep 16 18:13:11 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile CatD_0015_2_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other unweighted_spectral_entropy delta_RT_loess Found 4018 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 3539 positives and 479 negatives, size ratio=7.38831 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 28 as initial direction. Could separate 1847 training set positives with q<0.01 in that direction. Split 2: Selected feature 28 as initial direction. Could separate 1865 training set positives with q<0.01 in that direction. Split 3: Selected feature 28 as initial direction. Could separate 1880 training set positives with q<0.01 in that direction. Found 2788 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 2.2672 cpu seconds or 0 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 2983 PSMs with q<0.01 Iteration 2: Estimated 2995 PSMs with q<0.01 Iteration 3: Estimated 3002 PSMs with q<0.01 Iteration 4: Estimated 3004 PSMs with q<0.01 Iteration 5: Estimated 3008 PSMs with q<0.01 Iteration 6: Estimated 3011 PSMs with q<0.01 Iteration 7: Estimated 3012 PSMs with q<0.01 Iteration 8: Estimated 3012 PSMs with q<0.01 Iteration 9: Estimated 3012 PSMs with q<0.01 Iteration 10: Estimated 3012 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName 0.0000 0.0000 0.0000 rank -0.1492 -0.2248 -0.1011 abs_ppm -0.0327 -0.0387 -0.1724 isotope_errors -0.8206 -0.7425 -1.9095 log10_evalue 0.0330 -0.0573 -0.0371 hyperscore 0.3339 0.5710 -0.1556 delta_hyperscore 0.1054 0.0720 -0.7552 matched_ion_num -0.5049 -0.4795 -0.5699 complementary_ions -0.4912 -0.3046 -0.2735 ion_series -0.0324 -0.1315 -0.0643 weighted_average_abs_fragment_ppm 0.1435 -0.0053 -0.0229 length_7 -0.0105 0.0067 -0.0057 length_8 -0.0854 0.0093 0.0318 length_9_30 -0.0382 -0.0472 -0.0544 length_31 0.0000 0.0000 0.0000 ntt 0.0000 0.0000 0.0000 nmc 0.0000 0.0000 0.0000 charge_1 -0.1501 -0.2127 -0.1452 charge_2 0.0153 0.0451 0.0340 charge_3 0.1681 0.2181 0.1366 charge_4 0.0759 0.0416 0.0659 charge_5 -0.0135 -0.0167 -0.0192 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other 1.1563 1.2661 1.4378 unweighted_spectral_entropy -0.3889 -0.4136 -0.5859 delta_RT_loess 0.8558 1.0563 1.2180 m0 Found 2975 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 3539 target PSMs and 479 decoy PSMs. Calculating q values. Final list yields 2981 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 72.3378 cpu seconds or 50 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_3] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatA_0000_3_percolator_target_psms.tsv --decoy-results-psms CatA_0000_3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatA_0000_3_edited.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 09:42:23 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll (lukall@u.washington.edu) in the Department of Genome Sciences at the University of Washington. Issued command: /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatA_0000_3_percolator_target_psms.tsv --decoy-results-psms CatA_0000_3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatA_0000_3_edited.pin Started Mon Sep 16 18:14:01 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile CatA_0000_3_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other unweighted_spectral_entropy delta_RT_loess Found 5382 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 4837 positives and 545 negatives, size ratio=8.87523 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 28 as initial direction. Could separate 2738 training set positives with q<0.01 in that direction. Split 2: Selected feature 28 as initial direction. Could separate 2715 training set positives with q<0.01 in that direction. Split 3: Selected feature 28 as initial direction. Could separate 2715 training set positives with q<0.01 in that direction. Found 4081 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 2.1247 cpu seconds or 0 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 4282 PSMs with q<0.01 Iteration 2: Estimated 4294 PSMs with q<0.01 Iteration 3: Estimated 4300 PSMs with q<0.01 Iteration 4: Estimated 4301 PSMs with q<0.01 Iteration 5: Estimated 4301 PSMs with q<0.01 Iteration 6: Estimated 4301 PSMs with q<0.01 Iteration 7: Estimated 4301 PSMs with q<0.01 Iteration 8: Estimated 4301 PSMs with q<0.01 Iteration 9: Estimated 4301 PSMs with q<0.01 Iteration 10: Estimated 4301 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName 0.0000 0.0000 0.0000 rank -0.1738 -0.1757 -0.2048 abs_ppm 0.1063 0.0694 -0.0341 isotope_errors -0.9841 -1.7713 -0.9344 log10_evalue -0.1914 -1.0823 0.7784 hyperscore 0.3093 0.5349 0.1499 delta_hyperscore 0.3891 0.9637 -0.1290 matched_ion_num -0.6694 -1.1672 -1.1042 complementary_ions -0.6723 -0.8298 -0.0008 ion_series -0.1759 -0.1563 0.0094 weighted_average_abs_fragment_ppm 0.0712 0.0215 -0.0449 length_7 0.0767 -0.0181 0.1137 length_8 -0.0881 0.0146 -0.0270 length_9_30 -0.0422 -0.0574 -0.0671 length_31 0.0000 0.0000 0.0000 ntt 0.0000 0.0000 0.0000 nmc 0.0000 0.0000 0.0000 charge_1 -0.1662 -0.0682 -0.2265 charge_2 0.0875 0.1133 0.0830 charge_3 0.0726 -0.0945 0.1584 charge_4 0.0965 0.1361 0.0804 charge_5 0.0000 0.0000 0.0000 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other 1.1262 1.8262 1.1520 unweighted_spectral_entropy -0.4102 -0.5742 -0.4667 delta_RT_loess 1.0929 1.4876 1.7392 m0 Found 4285 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 4837 target PSMs and 545 decoy PSMs. Calculating q values. Final list yields 4285 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 20.3209 cpu seconds or 11 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_2] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatC_0090_2_percolator_target_psms.tsv --decoy-results-psms CatC_0090_2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatC_0090_2_edited.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 09:42:23 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll (lukall@u.washington.edu) in the Department of Genome Sciences at the University of Washington. Issued command: /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatC_0090_2_percolator_target_psms.tsv --decoy-results-psms CatC_0090_2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatC_0090_2_edited.pin Started Mon Sep 16 18:14:12 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile CatC_0090_2_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other unweighted_spectral_entropy delta_RT_loess Found 7358 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 6416 positives and 942 negatives, size ratio=6.81104 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 28 as initial direction. Could separate 3437 training set positives with q<0.01 in that direction. Split 2: Selected feature 28 as initial direction. Could separate 3424 training set positives with q<0.01 in that direction. Split 3: Selected feature 28 as initial direction. Could separate 3522 training set positives with q<0.01 in that direction. Found 5175 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 3.0854 cpu seconds or 0 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 5392 PSMs with q<0.01 Iteration 2: Estimated 5426 PSMs with q<0.01 Iteration 3: Estimated 5431 PSMs with q<0.01 Iteration 4: Estimated 5431 PSMs with q<0.01 Iteration 5: Estimated 5426 PSMs with q<0.01 Iteration 6: Estimated 5430 PSMs with q<0.01 Iteration 7: Estimated 5430 PSMs with q<0.01 Iteration 8: Estimated 5430 PSMs with q<0.01 Iteration 9: Estimated 5431 PSMs with q<0.01 Iteration 10: Estimated 5431 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName 0.0000 0.0000 0.0000 rank -0.2854 -0.2902 -0.4323 abs_ppm -0.0673 -0.1101 -0.1250 isotope_errors -0.6706 -0.7553 -0.7346 log10_evalue 0.1784 0.2085 0.8255 hyperscore 0.4589 0.2590 0.1259 delta_hyperscore 0.4525 0.1659 -0.4155 matched_ion_num -0.6330 -0.4925 -0.4201 complementary_ions -0.6047 -0.6539 -0.2927 ion_series -0.0085 -0.0193 -0.0139 weighted_average_abs_fragment_ppm 0.0005 -0.0145 -0.0742 length_7 -0.0209 0.0531 -0.0214 length_8 0.0496 0.0361 0.0986 length_9_30 -0.0834 -0.1369 -0.0840 length_31 0.0000 0.0000 0.0000 ntt 0.0000 0.0000 0.0000 nmc 0.0000 0.0000 0.0000 charge_1 -0.0888 -0.1120 -0.1588 charge_2 0.0266 0.0599 0.0436 charge_3 0.0597 0.0261 0.1010 charge_4 0.1024 0.1841 0.2361 charge_5 -0.0121 -0.0095 -0.0158 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other 1.2388 1.3882 1.6377 unweighted_spectral_entropy -0.4234 -0.4461 -0.5402 delta_RT_loess 1.0352 0.8175 1.3590 m0 Found 5418 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 6416 target PSMs and 942 decoy PSMs. Calculating q values. Final list yields 5418 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 16.6218 cpu seconds or 5 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_3] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatC_0000_3_percolator_target_psms.tsv --decoy-results-psms CatC_0000_3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatC_0000_3_edited.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 09:42:23 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll (lukall@u.washington.edu) in the Department of Genome Sciences at the University of Washington. Issued command: /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatC_0000_3_percolator_target_psms.tsv --decoy-results-psms CatC_0000_3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatC_0000_3_edited.pin Started Mon Sep 16 18:14:17 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile CatC_0000_3_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other unweighted_spectral_entropy delta_RT_loess Found 7151 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 6243 positives and 908 negatives, size ratio=6.87555 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 28 as initial direction. Could separate 3408 training set positives with q<0.01 in that direction. Split 2: Selected feature 28 as initial direction. Could separate 3347 training set positives with q<0.01 in that direction. Split 3: Selected feature 28 as initial direction. Could separate 3423 training set positives with q<0.01 in that direction. Found 5053 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 2.7454 cpu seconds or 1 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 5358 PSMs with q<0.01 Iteration 2: Estimated 5378 PSMs with q<0.01 Iteration 3: Estimated 5385 PSMs with q<0.01 Iteration 4: Estimated 5387 PSMs with q<0.01 Iteration 5: Estimated 5387 PSMs with q<0.01 Iteration 6: Estimated 5392 PSMs with q<0.01 Iteration 7: Estimated 5392 PSMs with q<0.01 Iteration 8: Estimated 5389 PSMs with q<0.01 Iteration 9: Estimated 5392 PSMs with q<0.01 Iteration 10: Estimated 5392 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName 0.0000 0.0000 0.0000 rank -0.3134 -0.2627 -0.1870 abs_ppm -0.0339 -0.0433 -0.0534 isotope_errors -1.1630 -1.0956 -0.9801 log10_evalue 0.3048 -0.0242 0.0105 hyperscore 0.1874 0.3948 0.3192 delta_hyperscore 0.1142 0.2905 -0.0109 matched_ion_num -0.7069 -0.7700 -0.5487 complementary_ions -0.6017 -0.5070 -0.5844 ion_series -0.0598 -0.0583 -0.1040 weighted_average_abs_fragment_ppm -0.0208 0.0007 0.0927 length_7 -0.0087 -0.0072 -0.0644 length_8 0.0648 0.0477 0.0180 length_9_30 -0.0869 -0.0814 -0.0692 length_31 0.0000 0.0000 0.0000 ntt 0.0000 0.0000 0.0000 nmc 0.0000 0.0000 0.0000 charge_1 -0.0641 -0.1120 -0.1357 charge_2 -0.0595 -0.0002 -0.0450 charge_3 0.1292 0.1143 0.2022 charge_4 0.1917 0.1629 0.1983 charge_5 0.0000 0.0000 0.0000 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other 1.1581 0.9972 1.1406 unweighted_spectral_entropy -0.3190 -0.4617 -0.4155 delta_RT_loess 1.1585 1.0856 0.9230 m0 Found 5384 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 6243 target PSMs and 908 decoy PSMs. Calculating q values. Final list yields 5385 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 20.5296 cpu seconds or 9 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatA_0000_1_percolator_target_psms.tsv --decoy-results-psms CatA_0000_1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatA_0000_1_edited.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 09:42:23 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll (lukall@u.washington.edu) in the Department of Genome Sciences at the University of Washington. Issued command: /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatA_0000_1_percolator_target_psms.tsv --decoy-results-psms CatA_0000_1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatA_0000_1_edited.pin Started Mon Sep 16 18:14:27 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile CatA_0000_1_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other unweighted_spectral_entropy delta_RT_loess Found 5372 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 4846 positives and 526 negatives, size ratio=9.21293 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 28 as initial direction. Could separate 2739 training set positives with q<0.01 in that direction. Split 2: Selected feature 28 as initial direction. Could separate 2720 training set positives with q<0.01 in that direction. Split 3: Selected feature 28 as initial direction. Could separate 2723 training set positives with q<0.01 in that direction. Found 4059 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 2.6712 cpu seconds or 0 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 4311 PSMs with q<0.01 Iteration 2: Estimated 4325 PSMs with q<0.01 Iteration 3: Estimated 4330 PSMs with q<0.01 Iteration 4: Estimated 4337 PSMs with q<0.01 Iteration 5: Estimated 4332 PSMs with q<0.01 Iteration 6: Estimated 4332 PSMs with q<0.01 Iteration 7: Estimated 4332 PSMs with q<0.01 Iteration 8: Estimated 4333 PSMs with q<0.01 Iteration 9: Estimated 4333 PSMs with q<0.01 Iteration 10: Estimated 4332 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName 0.0000 0.0000 0.0000 rank -0.2620 -0.1849 -0.2536 abs_ppm -0.0758 -0.0195 0.0162 isotope_errors -0.9395 -0.9395 -0.6461 log10_evalue 0.2209 0.0577 -0.0838 hyperscore -0.0347 0.3732 0.2922 delta_hyperscore -0.0641 0.0990 0.2973 matched_ion_num -0.7103 -0.5820 -0.5452 complementary_ions -0.1142 -0.6134 -0.3604 ion_series -0.0711 0.0009 -0.0812 weighted_average_abs_fragment_ppm 0.0029 0.0151 0.0161 length_7 -0.0319 0.0596 -0.0535 length_8 0.0272 -0.0468 0.0333 length_9_30 -0.0303 -0.0298 -0.0277 length_31 0.0000 0.0000 0.0000 ntt 0.0000 0.0000 0.0000 nmc 0.0000 0.0000 0.0000 charge_1 -0.1409 -0.0873 -0.0833 charge_2 0.0274 0.0475 0.0722 charge_3 0.1166 0.0164 -0.0110 charge_4 0.1259 0.1475 0.0881 charge_5 -0.0152 -0.0149 -0.0138 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other 0.8489 0.9097 0.8864 unweighted_spectral_entropy -0.5073 -0.4192 -0.4388 delta_RT_loess 1.1116 1.0921 1.0143 m0 Found 4317 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 4846 target PSMs and 526 decoy PSMs. Calculating q values. Final list yields 4326 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 18.5451 cpu seconds or 9 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_4] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatC_0000_4_percolator_target_psms.tsv --decoy-results-psms CatC_0000_4_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatC_0000_4_edited.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 09:42:23 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll (lukall@u.washington.edu) in the Department of Genome Sciences at the University of Washington. Issued command: /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatC_0000_4_percolator_target_psms.tsv --decoy-results-psms CatC_0000_4_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatC_0000_4_edited.pin Started Mon Sep 16 18:14:36 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile CatC_0000_4_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other unweighted_spectral_entropy delta_RT_loess Found 7361 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 6458 positives and 903 negatives, size ratio=7.15172 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 28 as initial direction. Could separate 3462 training set positives with q<0.01 in that direction. Split 2: Selected feature 28 as initial direction. Could separate 3478 training set positives with q<0.01 in that direction. Split 3: Selected feature 28 as initial direction. Could separate 3506 training set positives with q<0.01 in that direction. Found 5224 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 7.2621 cpu seconds or 1 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 5475 PSMs with q<0.01 Iteration 2: Estimated 5496 PSMs with q<0.01 Iteration 3: Estimated 5507 PSMs with q<0.01 Iteration 4: Estimated 5508 PSMs with q<0.01 Iteration 5: Estimated 5511 PSMs with q<0.01 Iteration 6: Estimated 5510 PSMs with q<0.01 Iteration 7: Estimated 5510 PSMs with q<0.01 Iteration 8: Estimated 5510 PSMs with q<0.01 Iteration 9: Estimated 5510 PSMs with q<0.01 Iteration 10: Estimated 5510 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName 0.0000 0.0000 0.0000 rank -0.2297 -0.1019 -0.2259 abs_ppm -0.1033 -0.1022 -0.0631 isotope_errors -1.9499 -1.5788 -1.4765 log10_evalue -1.0264 -0.9452 -0.3881 hyperscore 0.5340 0.7911 0.5517 delta_hyperscore 0.3234 0.3142 0.5586 matched_ion_num -0.6923 -0.3867 -0.8739 complementary_ions -0.4481 -0.5499 -0.7026 ion_series -0.0565 -0.1246 -0.0284 weighted_average_abs_fragment_ppm 0.0047 -0.0409 -0.0329 length_7 -0.0135 0.0617 -0.0379 length_8 0.0450 0.0310 -0.0083 length_9_30 -0.0813 -0.0945 0.1091 length_31 0.0000 0.0000 0.0000 ntt 0.0000 0.0000 0.0000 nmc 0.0000 0.0000 0.0000 charge_1 -0.1698 -0.1769 -0.0838 charge_2 0.0586 -0.0113 0.0348 charge_3 0.1176 0.2344 0.0464 charge_4 0.0936 0.0413 0.0636 charge_5 -0.0148 -0.0172 -0.0166 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other 1.2478 1.4347 1.1512 unweighted_spectral_entropy -0.3776 -0.5316 -0.3857 delta_RT_loess 1.2706 1.4768 1.4229 m0 Found 5485 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 6458 target PSMs and 903 decoy PSMs. Calculating q values. Final list yields 5485 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 20.4821 cpu seconds or 5 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_2] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatB_0015_2_percolator_target_psms.tsv --decoy-results-psms CatB_0015_2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatB_0015_2_edited.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 09:42:23 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll (lukall@u.washington.edu) in the Department of Genome Sciences at the University of Washington. Issued command: /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatB_0015_2_percolator_target_psms.tsv --decoy-results-psms CatB_0015_2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatB_0015_2_edited.pin Started Mon Sep 16 18:14:42 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile CatB_0015_2_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other unweighted_spectral_entropy delta_RT_loess Found 6606 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 5357 positives and 1249 negatives, size ratio=4.28903 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 28 as initial direction. Could separate 2486 training set positives with q<0.01 in that direction. Split 2: Selected feature 28 as initial direction. Could separate 2469 training set positives with q<0.01 in that direction. Split 3: Selected feature 28 as initial direction. Could separate 2512 training set positives with q<0.01 in that direction. Found 3723 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 2.6870 cpu seconds or 0 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 3994 PSMs with q<0.01 Iteration 2: Estimated 4019 PSMs with q<0.01 Iteration 3: Estimated 4017 PSMs with q<0.01 Iteration 4: Estimated 4020 PSMs with q<0.01 Iteration 5: Estimated 4022 PSMs with q<0.01 Iteration 6: Estimated 4020 PSMs with q<0.01 Iteration 7: Estimated 4020 PSMs with q<0.01 Iteration 8: Estimated 4018 PSMs with q<0.01 Iteration 9: Estimated 4018 PSMs with q<0.01 Iteration 10: Estimated 4019 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName 0.0000 0.0000 0.0000 rank -0.1486 -0.0977 -0.0906 abs_ppm -0.1095 -0.0938 -0.2203 isotope_errors -1.0408 -1.5844 -1.4515 log10_evalue 0.4894 -0.2021 0.1323 hyperscore 0.5317 0.2591 0.4856 delta_hyperscore 0.2132 0.6205 0.2984 matched_ion_num -0.9742 -0.7998 -0.8396 complementary_ions -0.4093 -0.7287 -0.8522 ion_series -0.0800 -0.0566 -0.0492 weighted_average_abs_fragment_ppm -0.0407 -0.0309 -0.0372 length_7 0.0954 0.0795 0.0778 length_8 -0.0015 0.0191 -0.0071 length_9_30 -0.0731 -0.1057 -0.0429 length_31 0.0000 0.0000 0.0000 ntt 0.0000 0.0000 0.0000 nmc 0.0000 0.0000 0.0000 charge_1 -0.0574 -0.1115 -0.1086 charge_2 0.0421 0.0378 0.0716 charge_3 0.0414 0.1308 0.0728 charge_4 -0.0613 -0.0297 -0.0492 charge_5 -0.0143 -0.0098 -0.0107 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other 1.2117 1.9147 1.6415 unweighted_spectral_entropy -0.5387 -0.7311 -0.4747 delta_RT_loess 0.8217 0.5654 0.6148 m0 Found 3994 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 5357 target PSMs and 1249 decoy PSMs. Calculating q values. Final list yields 3994 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 21.2218 cpu seconds or 12 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_4] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatB_0015_4_percolator_target_psms.tsv --decoy-results-psms CatB_0015_4_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatB_0015_4_edited.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 09:42:23 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll (lukall@u.washington.edu) in the Department of Genome Sciences at the University of Washington. Issued command: /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatB_0015_4_percolator_target_psms.tsv --decoy-results-psms CatB_0015_4_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatB_0015_4_edited.pin Started Mon Sep 16 18:14:54 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile CatB_0015_4_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other unweighted_spectral_entropy delta_RT_loess Found 6971 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 5699 positives and 1272 negatives, size ratio=4.48035 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 28 as initial direction. Could separate 2731 training set positives with q<0.01 in that direction. Split 2: Selected feature 28 as initial direction. Could separate 2743 training set positives with q<0.01 in that direction. Split 3: Selected feature 28 as initial direction. Could separate 2659 training set positives with q<0.01 in that direction. Found 4020 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 3.5668 cpu seconds or 0 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 4263 PSMs with q<0.01 Iteration 2: Estimated 4294 PSMs with q<0.01 Iteration 3: Estimated 4309 PSMs with q<0.01 Iteration 4: Estimated 4310 PSMs with q<0.01 Iteration 5: Estimated 4309 PSMs with q<0.01 Iteration 6: Estimated 4310 PSMs with q<0.01 Iteration 7: Estimated 4310 PSMs with q<0.01 Iteration 8: Estimated 4310 PSMs with q<0.01 Iteration 9: Estimated 4310 PSMs with q<0.01 Iteration 10: Estimated 4310 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName 0.0000 0.0000 0.0000 rank -0.1171 -0.1207 -0.0401 abs_ppm -0.1611 -0.2143 -0.2048 isotope_errors -0.7308 -0.9313 -1.0088 log10_evalue 0.1853 -0.2526 -0.3104 hyperscore 0.5409 0.7574 1.0082 delta_hyperscore 0.3565 0.5475 0.6585 matched_ion_num -0.5127 -0.6942 -0.8042 complementary_ions -0.3602 -0.5207 -0.2651 ion_series 0.0081 -0.0639 -0.0982 weighted_average_abs_fragment_ppm -0.0692 -0.0358 -0.0152 length_7 0.0847 0.0832 0.0844 length_8 0.0101 -0.0068 -0.0212 length_9_30 -0.0510 -0.0568 -0.0544 length_31 0.0000 0.0000 0.0000 ntt 0.0000 0.0000 0.0000 nmc 0.0000 0.0000 0.0000 charge_1 -0.0721 -0.0906 -0.1771 charge_2 -0.0117 0.0334 0.0737 charge_3 0.1219 0.0577 0.1416 charge_4 0.0093 0.0992 0.0209 charge_5 -0.0134 -0.0125 -0.0101 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other 1.3215 1.2597 1.4442 unweighted_spectral_entropy -0.2763 -0.1588 -0.1496 delta_RT_loess 0.7891 0.7371 0.5988 m0 Found 4240 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 5699 target PSMs and 1272 decoy PSMs. Calculating q values. Final list yields 4255 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 22.2526 cpu seconds or 6 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_1] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatB_0000_1_percolator_target_psms.tsv --decoy-results-psms CatB_0000_1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatB_0000_1_edited.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 09:42:23 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll (lukall@u.washington.edu) in the Department of Genome Sciences at the University of Washington. Issued command: /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatB_0000_1_percolator_target_psms.tsv --decoy-results-psms CatB_0000_1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatB_0000_1_edited.pin Started Mon Sep 16 18:15:00 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile CatB_0000_1_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other unweighted_spectral_entropy delta_RT_loess Found 5949 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 4781 positives and 1168 negatives, size ratio=4.09332 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 28 as initial direction. Could separate 2201 training set positives with q<0.01 in that direction. Split 2: Selected feature 28 as initial direction. Could separate 2218 training set positives with q<0.01 in that direction. Split 3: Selected feature 28 as initial direction. Could separate 2135 training set positives with q<0.01 in that direction. Found 3229 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 2.4839 cpu seconds or 0 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 3532 PSMs with q<0.01 Iteration 2: Estimated 3569 PSMs with q<0.01 Iteration 3: Estimated 3579 PSMs with q<0.01 Iteration 4: Estimated 3584 PSMs with q<0.01 Iteration 5: Estimated 3592 PSMs with q<0.01 Iteration 6: Estimated 3587 PSMs with q<0.01 Iteration 7: Estimated 3590 PSMs with q<0.01 Iteration 8: Estimated 3587 PSMs with q<0.01 Iteration 9: Estimated 3590 PSMs with q<0.01 Iteration 10: Estimated 3587 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName 0.0000 0.0000 0.0000 rank -0.1157 -0.1069 -0.3010 abs_ppm -0.0913 -0.0393 -0.0159 isotope_errors -0.9011 -1.0000 -0.9824 log10_evalue 0.4991 0.2004 0.6470 hyperscore 0.1221 0.1302 0.0403 delta_hyperscore 0.1111 0.0010 0.1531 matched_ion_num -0.6570 -0.4342 -0.4566 complementary_ions -0.1399 0.0825 -0.2174 ion_series 0.0119 -0.0175 -0.0026 weighted_average_abs_fragment_ppm -0.0464 -0.0599 -0.0334 length_7 0.2137 0.2123 0.0405 length_8 -0.0873 -0.0296 0.0205 length_9_30 -0.0483 -0.1513 -0.0559 length_31 0.0000 0.0000 0.0000 ntt 0.0000 0.0000 0.0000 nmc 0.0000 0.0000 0.0000 charge_1 -0.0790 -0.0479 -0.0460 charge_2 0.0405 0.0412 0.0469 charge_3 0.0415 -0.0220 0.0188 charge_4 0.0424 0.0916 -0.0731 charge_5 -0.0088 -0.0097 -0.0107 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other 1.3418 1.4328 1.2913 unweighted_spectral_entropy -0.6087 -0.9316 -0.7006 delta_RT_loess 0.6786 0.7477 0.8282 m0 Found 3546 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 4781 target PSMs and 1168 decoy PSMs. Calculating q values. Final list yields 3547 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 13.3463 cpu seconds or 5 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_1] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatA_0090_1_percolator_target_psms.tsv --decoy-results-psms CatA_0090_1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatA_0090_1_edited.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 09:42:23 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll (lukall@u.washington.edu) in the Department of Genome Sciences at the University of Washington. Issued command: /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatA_0090_1_percolator_target_psms.tsv --decoy-results-psms CatA_0090_1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatA_0090_1_edited.pin Started Mon Sep 16 18:15:05 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile CatA_0090_1_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other unweighted_spectral_entropy delta_RT_loess Found 4974 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 4607 positives and 367 negatives, size ratio=12.5531 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 28 as initial direction. Could separate 2750 training set positives with q<0.01 in that direction. Split 2: Selected feature 28 as initial direction. Could separate 2715 training set positives with q<0.01 in that direction. Split 3: Selected feature 28 as initial direction. Could separate 2771 training set positives with q<0.01 in that direction. Found 4111 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 2.6658 cpu seconds or 0 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 4250 PSMs with q<0.01 Iteration 2: Estimated 4255 PSMs with q<0.01 Iteration 3: Estimated 4251 PSMs with q<0.01 Iteration 4: Estimated 4251 PSMs with q<0.01 Iteration 5: Estimated 4250 PSMs with q<0.01 Iteration 6: Estimated 4254 PSMs with q<0.01 Iteration 7: Estimated 4254 PSMs with q<0.01 Iteration 8: Estimated 4254 PSMs with q<0.01 Iteration 9: Estimated 4254 PSMs with q<0.01 Iteration 10: Estimated 4254 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName 0.0000 0.0000 0.0000 rank -0.0433 -0.1680 -0.1619 abs_ppm 0.0133 -0.0029 0.0117 isotope_errors -0.6767 -0.4922 -0.4118 log10_evalue 0.3047 0.7289 0.0156 hyperscore 0.2657 0.0342 0.2087 delta_hyperscore -0.1248 -0.5513 0.6548 matched_ion_num -0.7068 -0.4006 -0.7745 complementary_ions -0.3993 -0.3604 -0.6859 ion_series 0.0220 -0.0842 -0.0036 weighted_average_abs_fragment_ppm 0.1947 -0.0327 -0.0436 length_7 -0.0801 -0.0396 0.1452 length_8 -0.0653 0.0580 -0.0667 length_9_30 -0.0494 -0.0365 -0.0336 length_31 0.0000 0.0000 0.0000 ntt 0.0000 0.0000 0.0000 nmc 0.0000 0.0000 0.0000 charge_1 -0.1771 -0.1155 -0.1364 charge_2 0.0069 0.0504 0.0429 charge_3 0.1865 0.0741 0.0868 charge_4 0.1472 0.0135 0.1516 charge_5 0.0000 0.0000 0.0000 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other 0.9416 0.9906 0.8986 unweighted_spectral_entropy -0.6202 -0.5397 -0.5384 delta_RT_loess 1.1421 1.1491 1.0578 m0 Found 4238 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 4607 target PSMs and 367 decoy PSMs. Calculating q values. Final list yields 4249 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 79.1278 cpu seconds or 54 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_4] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatA_0090_4_percolator_target_psms.tsv --decoy-results-psms CatA_0090_4_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatA_0090_4_edited.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 09:42:23 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll (lukall@u.washington.edu) in the Department of Genome Sciences at the University of Washington. Issued command: /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatA_0090_4_percolator_target_psms.tsv --decoy-results-psms CatA_0090_4_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatA_0090_4_edited.pin Started Mon Sep 16 18:15:59 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile CatA_0090_4_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other unweighted_spectral_entropy delta_RT_loess Found 4955 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 4559 positives and 396 negatives, size ratio=11.5126 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 28 as initial direction. Could separate 2660 training set positives with q<0.01 in that direction. Split 2: Selected feature 28 as initial direction. Could separate 2658 training set positives with q<0.01 in that direction. Split 3: Selected feature 28 as initial direction. Could separate 2629 training set positives with q<0.01 in that direction. Found 3969 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 1.9717 cpu seconds or 0 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 4131 PSMs with q<0.01 Iteration 2: Estimated 4148 PSMs with q<0.01 Iteration 3: Estimated 4152 PSMs with q<0.01 Iteration 4: Estimated 4154 PSMs with q<0.01 Iteration 5: Estimated 4156 PSMs with q<0.01 Iteration 6: Estimated 4157 PSMs with q<0.01 Iteration 7: Estimated 4158 PSMs with q<0.01 Iteration 8: Estimated 4158 PSMs with q<0.01 Iteration 9: Estimated 4158 PSMs with q<0.01 Iteration 10: Estimated 4158 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName 0.0000 0.0000 0.0000 rank -0.1639 -0.2872 -0.2311 abs_ppm -0.1005 -0.1106 -0.1232 isotope_errors -0.8242 -0.9418 -0.9460 log10_evalue 0.2242 0.0230 -0.0608 hyperscore 0.0769 -0.0353 0.5779 delta_hyperscore -0.0205 -0.0103 0.4631 matched_ion_num -0.7124 -0.8279 -0.5526 complementary_ions -0.2784 0.1310 -0.6714 ion_series 0.0132 -0.1257 0.0108 weighted_average_abs_fragment_ppm 0.1604 -0.0918 0.0030 length_7 -0.0816 0.2255 -0.0354 length_8 -0.0548 -0.0836 0.0286 length_9_30 -0.0264 -0.0303 -0.0390 length_31 0.0000 0.0000 0.0000 ntt 0.0000 0.0000 0.0000 nmc 0.0000 0.0000 0.0000 charge_1 -0.0853 -0.1063 -0.1673 charge_2 -0.0393 0.0484 0.0481 charge_3 0.1368 0.0651 0.1332 charge_4 0.1500 0.0316 0.0915 charge_5 -0.0152 -0.0175 -0.0225 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other 0.7872 0.7688 1.0430 unweighted_spectral_entropy -0.4065 -0.4358 -0.4497 delta_RT_loess 1.0721 1.2323 1.5848 m0 Found 4133 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 4559 target PSMs and 396 decoy PSMs. Calculating q values. Final list yields 4140 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 32.1402 cpu seconds or 19 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_1] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatC_0000_1_percolator_target_psms.tsv --decoy-results-psms CatC_0000_1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatC_0000_1_edited.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 09:42:23 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll (lukall@u.washington.edu) in the Department of Genome Sciences at the University of Washington. Issued command: /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatC_0000_1_percolator_target_psms.tsv --decoy-results-psms CatC_0000_1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatC_0000_1_edited.pin Started Mon Sep 16 18:16:18 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile CatC_0000_1_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other unweighted_spectral_entropy delta_RT_loess Found 7096 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 6246 positives and 850 negatives, size ratio=7.34824 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 28 as initial direction. Could separate 3293 training set positives with q<0.01 in that direction. Split 2: Selected feature 28 as initial direction. Could separate 3418 training set positives with q<0.01 in that direction. Split 3: Selected feature 28 as initial direction. Could separate 3421 training set positives with q<0.01 in that direction. Found 5048 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 2.7225 cpu seconds or 0 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 5315 PSMs with q<0.01 Iteration 2: Estimated 5343 PSMs with q<0.01 Iteration 3: Estimated 5348 PSMs with q<0.01 Iteration 4: Estimated 5350 PSMs with q<0.01 Iteration 5: Estimated 5349 PSMs with q<0.01 Iteration 6: Estimated 5347 PSMs with q<0.01 Iteration 7: Estimated 5347 PSMs with q<0.01 Iteration 8: Estimated 5347 PSMs with q<0.01 Iteration 9: Estimated 5347 PSMs with q<0.01 Iteration 10: Estimated 5347 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName 0.0000 0.0000 0.0000 rank -0.1789 -0.2810 -0.2262 abs_ppm -0.0791 -0.0716 -0.1050 isotope_errors -1.1796 -1.0889 -1.7887 log10_evalue -0.3104 0.0353 -0.8490 hyperscore 0.5409 0.7588 0.9065 delta_hyperscore 0.0558 0.0773 0.2620 matched_ion_num -0.6179 -0.7802 -0.6380 complementary_ions -0.2878 -0.3905 -0.4969 ion_series 0.0014 -0.0241 0.0797 weighted_average_abs_fragment_ppm -0.0317 0.2084 0.0055 length_7 0.0987 -0.0187 0.0351 length_8 0.0005 -0.0706 0.0178 length_9_30 -0.0899 -0.0936 -0.0896 length_31 0.0000 0.0000 0.0000 ntt 0.0000 0.0000 0.0000 nmc 0.0000 0.0000 0.0000 charge_1 -0.0461 -0.0812 -0.0235 charge_2 0.0708 0.0112 0.0682 charge_3 -0.0666 0.0580 -0.0957 charge_4 0.1327 0.1721 0.1460 charge_5 -0.0129 -0.0177 -0.0169 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other 1.0912 1.2430 1.1444 unweighted_spectral_entropy -0.4319 -0.4175 -0.4243 delta_RT_loess 1.0905 1.4876 1.4230 m0 Found 5307 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 6246 target PSMs and 850 decoy PSMs. Calculating q values. Final list yields 5307 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 23.9363 cpu seconds or 13 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_1] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatC_0030_1_percolator_target_psms.tsv --decoy-results-psms CatC_0030_1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatC_0030_1_edited.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 09:42:23 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll (lukall@u.washington.edu) in the Department of Genome Sciences at the University of Washington. Issued command: /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatC_0030_1_percolator_target_psms.tsv --decoy-results-psms CatC_0030_1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatC_0030_1_edited.pin Started Mon Sep 16 18:16:31 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile CatC_0030_1_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other unweighted_spectral_entropy delta_RT_loess Found 7081 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 6202 positives and 879 negatives, size ratio=7.05575 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 28 as initial direction. Could separate 3369 training set positives with q<0.01 in that direction. Split 2: Selected feature 28 as initial direction. Could separate 3277 training set positives with q<0.01 in that direction. Split 3: Selected feature 28 as initial direction. Could separate 3326 training set positives with q<0.01 in that direction. Found 4953 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 2.7939 cpu seconds or 0 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 5259 PSMs with q<0.01 Iteration 2: Estimated 5292 PSMs with q<0.01 Iteration 3: Estimated 5305 PSMs with q<0.01 Iteration 4: Estimated 5304 PSMs with q<0.01 Iteration 5: Estimated 5304 PSMs with q<0.01 Iteration 6: Estimated 5304 PSMs with q<0.01 Iteration 7: Estimated 5305 PSMs with q<0.01 Iteration 8: Estimated 5305 PSMs with q<0.01 Iteration 9: Estimated 5305 PSMs with q<0.01 Iteration 10: Estimated 5308 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName 0.0000 0.0000 0.0000 rank -0.1799 -0.1473 -0.2634 abs_ppm -0.1036 -0.1703 -0.1341 isotope_errors -0.9206 -1.3319 -1.0599 log10_evalue 0.0176 -0.2226 0.0493 hyperscore 0.3978 0.1889 0.2556 delta_hyperscore 0.1587 -0.0128 0.0246 matched_ion_num -0.6959 -0.7675 -0.5209 complementary_ions -0.5103 -0.1826 -0.5094 ion_series -0.0523 -0.1113 -0.0920 weighted_average_abs_fragment_ppm 0.0810 -0.0031 -0.0086 length_7 -0.0326 -0.0111 -0.0120 length_8 0.0066 0.0422 0.0477 length_9_30 -0.0624 -0.0640 -0.0673 length_31 0.0000 0.0000 0.0000 ntt 0.0000 0.0000 0.0000 nmc 0.0000 0.0000 0.0000 charge_1 -0.0844 -0.0533 -0.1182 charge_2 0.0153 0.0018 0.0815 charge_3 0.0761 0.0608 0.0267 charge_4 0.0688 0.0376 0.0705 charge_5 -0.0112 -0.0115 -0.0121 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other 1.0985 1.0673 1.1497 unweighted_spectral_entropy -0.4039 -0.4618 -0.4609 delta_RT_loess 0.9407 0.9654 1.0154 m0 Found 5275 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 6202 target PSMs and 879 decoy PSMs. Calculating q values. Final list yields 5288 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 26.7012 cpu seconds or 11 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_4] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatC_0090_4_percolator_target_psms.tsv --decoy-results-psms CatC_0090_4_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatC_0090_4_edited.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 09:42:23 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll (lukall@u.washington.edu) in the Department of Genome Sciences at the University of Washington. Issued command: /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatC_0090_4_percolator_target_psms.tsv --decoy-results-psms CatC_0090_4_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatC_0090_4_edited.pin Started Mon Sep 16 18:16:42 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile CatC_0090_4_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other unweighted_spectral_entropy delta_RT_loess Found 7543 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 6624 positives and 919 negatives, size ratio=7.20783 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 28 as initial direction. Could separate 3563 training set positives with q<0.01 in that direction. Split 2: Selected feature 28 as initial direction. Could separate 3611 training set positives with q<0.01 in that direction. Split 3: Selected feature 28 as initial direction. Could separate 3482 training set positives with q<0.01 in that direction. Found 5330 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 2.9254 cpu seconds or 0 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 5599 PSMs with q<0.01 Iteration 2: Estimated 5629 PSMs with q<0.01 Iteration 3: Estimated 5651 PSMs with q<0.01 Iteration 4: Estimated 5647 PSMs with q<0.01 Iteration 5: Estimated 5647 PSMs with q<0.01 Iteration 6: Estimated 5649 PSMs with q<0.01 Iteration 7: Estimated 5648 PSMs with q<0.01 Iteration 8: Estimated 5648 PSMs with q<0.01 Iteration 9: Estimated 5647 PSMs with q<0.01 Iteration 10: Estimated 5647 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName 0.0000 0.0000 0.0000 rank -0.4098 -0.3998 -0.3395 abs_ppm 0.0451 -0.0093 0.0786 isotope_errors -1.0303 -1.1662 -1.1892 log10_evalue -0.6521 -0.6803 -0.3527 hyperscore 0.3968 0.7144 0.6333 delta_hyperscore 0.6333 0.2345 -0.0401 matched_ion_num -0.7239 -0.6855 -0.4753 complementary_ions -0.4192 -0.0732 -0.3413 ion_series -0.1286 -0.0878 -0.0938 weighted_average_abs_fragment_ppm -0.0188 0.0961 -0.0409 length_7 -0.0207 -0.0346 0.0718 length_8 0.0478 -0.0056 -0.0025 length_9_30 -0.0548 -0.0715 -0.0554 length_31 0.0000 0.0000 0.0000 ntt 0.0000 0.0000 0.0000 nmc 0.0000 0.0000 0.0000 charge_1 -0.0781 -0.0345 -0.1440 charge_2 0.0161 0.0030 0.0203 charge_3 0.0747 0.0285 0.1600 charge_4 0.0395 0.0664 0.0321 charge_5 0.0000 0.0000 0.0000 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other 1.1866 1.1293 1.3007 unweighted_spectral_entropy -0.4245 -0.4433 -0.3384 delta_RT_loess 1.0128 1.3220 1.0246 m0 Found 5620 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 6624 target PSMs and 919 decoy PSMs. Calculating q values. Final list yields 5626 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 17.6572 cpu seconds or 6 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_2] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatC_0000_2_percolator_target_psms.tsv --decoy-results-psms CatC_0000_2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatC_0000_2_edited.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 09:42:23 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll (lukall@u.washington.edu) in the Department of Genome Sciences at the University of Washington. Issued command: /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatC_0000_2_percolator_target_psms.tsv --decoy-results-psms CatC_0000_2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatC_0000_2_edited.pin Started Mon Sep 16 18:16:48 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile CatC_0000_2_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other unweighted_spectral_entropy delta_RT_loess Found 7449 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 6496 positives and 953 negatives, size ratio=6.81637 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 28 as initial direction. Could separate 3429 training set positives with q<0.01 in that direction. Split 2: Selected feature 28 as initial direction. Could separate 3466 training set positives with q<0.01 in that direction. Split 3: Selected feature 28 as initial direction. Could separate 3492 training set positives with q<0.01 in that direction. Found 5170 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 3.1334 cpu seconds or 0 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 5495 PSMs with q<0.01 Iteration 2: Estimated 5544 PSMs with q<0.01 Iteration 3: Estimated 5557 PSMs with q<0.01 Iteration 4: Estimated 5556 PSMs with q<0.01 Iteration 5: Estimated 5559 PSMs with q<0.01 Iteration 6: Estimated 5560 PSMs with q<0.01 Iteration 7: Estimated 5560 PSMs with q<0.01 Iteration 8: Estimated 5560 PSMs with q<0.01 Iteration 9: Estimated 5560 PSMs with q<0.01 Iteration 10: Estimated 5560 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName 0.0000 0.0000 0.0000 rank -0.2569 -0.2152 -0.2399 abs_ppm -0.1148 -0.1402 -0.1306 isotope_errors -1.9218 -1.1850 -1.1486 log10_evalue -1.2132 -0.1212 -0.1485 hyperscore 0.7209 0.6744 0.5876 delta_hyperscore 0.4652 -0.0960 -0.1777 matched_ion_num -0.8518 -0.7136 -0.5254 complementary_ions -0.4818 -0.2035 -0.0531 ion_series -0.0544 -0.0163 0.0356 weighted_average_abs_fragment_ppm 0.0066 0.0877 0.0011 length_7 0.0391 -0.0196 -0.0047 length_8 0.0155 0.0022 0.0435 length_9_30 -0.0836 -0.0759 -0.0781 length_31 0.0000 0.0000 0.0000 ntt 0.0000 0.0000 0.0000 nmc 0.0000 0.0000 0.0000 charge_1 -0.1279 -0.1625 -0.1222 charge_2 0.0144 0.0724 0.0583 charge_3 0.1391 0.0997 0.0662 charge_4 0.0306 0.0463 0.0513 charge_5 -0.0205 -0.0186 -0.0192 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other 1.1044 1.0320 1.0217 unweighted_spectral_entropy -0.4084 -0.4235 -0.3471 delta_RT_loess 1.2532 1.1372 1.1703 m0 Found 5529 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 6496 target PSMs and 953 decoy PSMs. Calculating q values. Final list yields 5535 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 26.5984 cpu seconds or 11 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0000_1] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatD_0000_1_percolator_target_psms.tsv --decoy-results-psms CatD_0000_1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatD_0000_1_edited.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 09:42:23 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll (lukall@u.washington.edu) in the Department of Genome Sciences at the University of Washington. Issued command: /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatD_0000_1_percolator_target_psms.tsv --decoy-results-psms CatD_0000_1_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatD_0000_1_edited.pin Started Mon Sep 16 18:16:59 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile CatD_0000_1_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other unweighted_spectral_entropy delta_RT_loess Found 5495 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 4546 positives and 949 negatives, size ratio=4.79031 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 28 as initial direction. Could separate 2169 training set positives with q<0.01 in that direction. Split 2: Selected feature 28 as initial direction. Could separate 2182 training set positives with q<0.01 in that direction. Split 3: Selected feature 28 as initial direction. Could separate 2227 training set positives with q<0.01 in that direction. Found 3251 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 2.4888 cpu seconds or 0 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 3491 PSMs with q<0.01 Iteration 2: Estimated 3517 PSMs with q<0.01 Iteration 3: Estimated 3520 PSMs with q<0.01 Iteration 4: Estimated 3528 PSMs with q<0.01 Iteration 5: Estimated 3525 PSMs with q<0.01 Iteration 6: Estimated 3525 PSMs with q<0.01 Iteration 7: Estimated 3525 PSMs with q<0.01 Iteration 8: Estimated 3525 PSMs with q<0.01 Iteration 9: Estimated 3525 PSMs with q<0.01 Iteration 10: Estimated 3525 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName 0.0000 0.0000 0.0000 rank -0.2066 -0.0098 -0.1971 abs_ppm -0.1023 -0.1394 -0.1482 isotope_errors -0.9309 -1.7562 -1.1670 log10_evalue 0.3066 -0.3562 -0.1769 hyperscore 0.2214 0.6017 0.3946 delta_hyperscore 0.0328 0.2022 0.2449 matched_ion_num -0.6283 -0.7724 -0.6515 complementary_ions -0.2725 -0.2077 -0.2663 ion_series -0.0229 -0.1840 -0.1382 weighted_average_abs_fragment_ppm -0.0247 -0.0530 0.0190 length_7 0.0810 0.1538 0.0314 length_8 -0.0149 -0.0244 -0.0147 length_9_30 -0.0401 -0.0760 -0.0362 length_31 0.0000 0.0000 0.0000 ntt 0.0000 0.0000 0.0000 nmc 0.0000 0.0000 0.0000 charge_1 -0.0884 -0.1506 0.0362 charge_2 0.0600 0.0768 -0.0063 charge_3 0.0278 0.0337 -0.0435 charge_4 0.0173 0.2353 0.0270 charge_5 -0.0129 -0.0244 -0.0116 charge_6 -0.0074 -0.0141 -0.0067 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other 1.2829 1.8456 1.1587 unweighted_spectral_entropy -0.4553 -1.0456 -0.4779 delta_RT_loess 0.5506 1.0429 0.4965 m0 Found 3489 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 4546 target PSMs and 949 decoy PSMs. Calculating q values. Final list yields 3492 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 14.1955 cpu seconds or 5 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_4] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatB_0060_4_percolator_target_psms.tsv --decoy-results-psms CatB_0060_4_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatB_0060_4_edited.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 09:42:23 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll (lukall@u.washington.edu) in the Department of Genome Sciences at the University of Washington. Issued command: /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatB_0060_4_percolator_target_psms.tsv --decoy-results-psms CatB_0060_4_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatB_0060_4_edited.pin Started Mon Sep 16 18:17:04 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile CatB_0060_4_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other unweighted_spectral_entropy delta_RT_loess Found 6302 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 5266 positives and 1036 negatives, size ratio=5.08301 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 28 as initial direction. Could separate 2648 training set positives with q<0.01 in that direction. Split 2: Selected feature 28 as initial direction. Could separate 2608 training set positives with q<0.01 in that direction. Split 3: Selected feature 28 as initial direction. Could separate 2606 training set positives with q<0.01 in that direction. Found 3900 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 4.8717 cpu seconds or 0 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 4187 PSMs with q<0.01 Iteration 2: Estimated 4215 PSMs with q<0.01 Iteration 3: Estimated 4224 PSMs with q<0.01 Iteration 4: Estimated 4222 PSMs with q<0.01 Iteration 5: Estimated 4230 PSMs with q<0.01 Iteration 6: Estimated 4231 PSMs with q<0.01 Iteration 7: Estimated 4227 PSMs with q<0.01 Iteration 8: Estimated 4227 PSMs with q<0.01 Iteration 9: Estimated 4226 PSMs with q<0.01 Iteration 10: Estimated 4224 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName 0.0000 0.0000 0.0000 rank -0.1152 -0.1100 -0.0025 abs_ppm -0.0507 -0.0457 -0.0091 isotope_errors -1.1809 -1.2972 -1.4477 log10_evalue -0.1532 -0.7653 -0.9035 hyperscore 0.6972 1.1147 1.2519 delta_hyperscore 0.2036 0.4265 1.6741 matched_ion_num -0.8833 -0.7074 -0.5870 complementary_ions -0.4504 -0.5374 -1.2714 ion_series -0.0593 -0.1130 -0.2524 weighted_average_abs_fragment_ppm -0.0003 0.0265 0.0941 length_7 0.0218 0.0270 0.0152 length_8 0.0102 -0.0105 -0.0249 length_9_30 -0.0577 -0.0570 -0.1065 length_31 0.0000 0.0000 0.0000 ntt 0.0000 0.0000 0.0000 nmc 0.0000 0.0000 0.0000 charge_1 -0.1011 -0.1131 -0.2320 charge_2 0.0400 0.0656 0.0781 charge_3 0.0818 0.0557 0.2217 charge_4 0.0307 0.0489 0.0118 charge_5 -0.0163 -0.0161 -0.0301 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other 1.2715 1.5344 2.0468 unweighted_spectral_entropy -0.5307 -0.9565 -0.9557 delta_RT_loess 0.9139 0.9033 1.6870 m0 Found 4171 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 5266 target PSMs and 1036 decoy PSMs. Calculating q values. Final list yields 4178 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 15.4658 cpu seconds or 5 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_2] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatB_0000_2_percolator_target_psms.tsv --decoy-results-psms CatB_0000_2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatB_0000_2_edited.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 09:42:23 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll (lukall@u.washington.edu) in the Department of Genome Sciences at the University of Washington. Issued command: /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatB_0000_2_percolator_target_psms.tsv --decoy-results-psms CatB_0000_2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatB_0000_2_edited.pin Started Mon Sep 16 18:17:10 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile CatB_0000_2_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other unweighted_spectral_entropy delta_RT_loess Found 5530 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 4692 positives and 838 negatives, size ratio=5.59905 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 28 as initial direction. Could separate 2328 training set positives with q<0.01 in that direction. Split 2: Selected feature 28 as initial direction. Could separate 2356 training set positives with q<0.01 in that direction. Split 3: Selected feature 28 as initial direction. Could separate 2363 training set positives with q<0.01 in that direction. Found 3467 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 2.3212 cpu seconds or 0 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 3742 PSMs with q<0.01 Iteration 2: Estimated 3765 PSMs with q<0.01 Iteration 3: Estimated 3776 PSMs with q<0.01 Iteration 4: Estimated 3782 PSMs with q<0.01 Iteration 5: Estimated 3778 PSMs with q<0.01 Iteration 6: Estimated 3776 PSMs with q<0.01 Iteration 7: Estimated 3777 PSMs with q<0.01 Iteration 8: Estimated 3776 PSMs with q<0.01 Iteration 9: Estimated 3776 PSMs with q<0.01 Iteration 10: Estimated 3776 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName 0.0000 0.0000 0.0000 rank -0.2387 -0.2612 -0.3149 abs_ppm -0.0744 -0.0789 -0.0636 isotope_errors -1.1483 -1.0572 -1.6023 log10_evalue -0.0869 -0.0664 -0.3177 hyperscore 0.6825 0.5061 0.3464 delta_hyperscore -0.1646 -0.0437 0.2616 matched_ion_num -0.6531 -0.5034 -0.6852 complementary_ions -0.2057 -0.2313 -0.3706 ion_series 0.0594 -0.0573 0.0806 weighted_average_abs_fragment_ppm -0.1093 0.0272 -0.1054 length_7 0.1507 -0.0037 0.1421 length_8 0.0008 0.0173 0.0114 length_9_30 -0.0691 -0.0614 -0.0839 length_31 0.0000 0.0000 0.0000 ntt 0.0000 0.0000 0.0000 nmc 0.0000 0.0000 0.0000 charge_1 -0.0483 -0.0097 0.0090 charge_2 0.0921 0.0793 0.0618 charge_3 -0.0641 -0.1027 -0.1003 charge_4 -0.0316 -0.0258 -0.0385 charge_5 -0.0130 -0.0116 -0.0158 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other 1.2865 1.1443 1.4198 unweighted_spectral_entropy -0.5100 -0.5017 -0.4925 delta_RT_loess 0.9685 0.8610 1.1758 m0 Found 3760 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 4692 target PSMs and 838 decoy PSMs. Calculating q values. Final list yields 3762 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 26.6853 cpu seconds or 5 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_4] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatA_0000_4_percolator_target_psms.tsv --decoy-results-psms CatA_0000_4_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatA_0000_4_edited.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 09:42:23 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll (lukall@u.washington.edu) in the Department of Genome Sciences at the University of Washington. Issued command: /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatA_0000_4_percolator_target_psms.tsv --decoy-results-psms CatA_0000_4_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatA_0000_4_edited.pin Started Mon Sep 16 18:17:15 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile CatA_0000_4_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other unweighted_spectral_entropy delta_RT_loess Found 5456 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 4944 positives and 512 negatives, size ratio=9.65625 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 28 as initial direction. Could separate 2744 training set positives with q<0.01 in that direction. Split 2: Selected feature 28 as initial direction. Could separate 2733 training set positives with q<0.01 in that direction. Split 3: Selected feature 28 as initial direction. Could separate 2782 training set positives with q<0.01 in that direction. Found 4116 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 2.7676 cpu seconds or 0 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 4365 PSMs with q<0.01 Iteration 2: Estimated 4411 PSMs with q<0.01 Iteration 3: Estimated 4419 PSMs with q<0.01 Iteration 4: Estimated 4418 PSMs with q<0.01 Iteration 5: Estimated 4417 PSMs with q<0.01 Iteration 6: Estimated 4418 PSMs with q<0.01 Iteration 7: Estimated 4417 PSMs with q<0.01 Iteration 8: Estimated 4417 PSMs with q<0.01 Iteration 9: Estimated 4417 PSMs with q<0.01 Iteration 10: Estimated 4417 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName 0.0000 0.0000 0.0000 rank -0.2272 -0.1551 -0.1835 abs_ppm -0.0151 -0.0328 -0.0532 isotope_errors -1.8808 -0.7308 -1.0230 log10_evalue -0.3406 0.2566 -0.4163 hyperscore 0.0963 0.3903 0.2566 delta_hyperscore -0.1541 -0.4817 0.1557 matched_ion_num -0.6499 -0.5915 -0.5373 complementary_ions -0.4961 -0.1354 -0.1298 ion_series -0.1151 -0.1303 -0.1038 weighted_average_abs_fragment_ppm 0.0009 -0.0261 0.0588 length_7 -0.0177 -0.0760 -0.0954 length_8 0.0234 0.0819 0.0429 length_9_30 -0.0436 -0.0374 -0.0410 length_31 0.0000 0.0000 0.0000 ntt 0.0000 0.0000 0.0000 nmc 0.0000 0.0000 0.0000 charge_1 -0.1772 -0.1622 -0.1402 charge_2 0.0879 0.0175 0.0041 charge_3 0.0582 0.1268 0.1396 charge_4 0.2006 0.2409 0.1372 charge_5 0.0000 0.0000 0.0000 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other 1.0851 1.1415 0.9706 unweighted_spectral_entropy -0.4688 -0.4337 -0.3795 delta_RT_loess 1.3136 1.1283 1.2356 m0 Found 4417 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 4944 target PSMs and 512 decoy PSMs. Calculating q values. Final list yields 4420 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 35.4191 cpu seconds or 9 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_4] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatB_0000_4_percolator_target_psms.tsv --decoy-results-psms CatB_0000_4_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatB_0000_4_edited.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 09:42:23 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll (lukall@u.washington.edu) in the Department of Genome Sciences at the University of Washington. Issued command: /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatB_0000_4_percolator_target_psms.tsv --decoy-results-psms CatB_0000_4_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatB_0000_4_edited.pin Started Mon Sep 16 18:17:24 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile CatB_0000_4_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other unweighted_spectral_entropy delta_RT_loess Found 7397 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 5868 positives and 1529 negatives, size ratio=3.8378 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 28 as initial direction. Could separate 2620 training set positives with q<0.01 in that direction. Split 2: Selected feature 28 as initial direction. Could separate 2638 training set positives with q<0.01 in that direction. Split 3: Selected feature 28 as initial direction. Could separate 2532 training set positives with q<0.01 in that direction. Found 3858 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 3.2168 cpu seconds or 1 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 4172 PSMs with q<0.01 Iteration 2: Estimated 4225 PSMs with q<0.01 Iteration 3: Estimated 4248 PSMs with q<0.01 Iteration 4: Estimated 4246 PSMs with q<0.01 Iteration 5: Estimated 4252 PSMs with q<0.01 Iteration 6: Estimated 4245 PSMs with q<0.01 Iteration 7: Estimated 4250 PSMs with q<0.01 Iteration 8: Estimated 4248 PSMs with q<0.01 Iteration 9: Estimated 4247 PSMs with q<0.01 Iteration 10: Estimated 4247 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName 0.0000 0.0000 0.0000 rank -0.1454 -0.1063 -0.2301 abs_ppm -0.1800 -0.1141 -0.0906 isotope_errors -1.0942 -0.9420 -1.0328 log10_evalue -0.1198 -0.0973 -0.0608 hyperscore 0.6385 0.5943 0.6694 delta_hyperscore 0.5340 -0.0150 0.5046 matched_ion_num -0.7326 -0.5419 -0.8746 complementary_ions -0.5418 -0.1695 -0.5120 ion_series -0.1685 -0.1815 -0.2136 weighted_average_abs_fragment_ppm -0.0366 -0.0664 -0.0742 length_7 -0.0198 0.0082 -0.0182 length_8 -0.0037 0.0387 0.0089 length_9_30 0.0624 -0.0143 0.0739 length_31 0.0000 0.0000 0.0000 ntt 0.0000 0.0000 0.0000 nmc 0.0000 0.0000 0.0000 charge_1 -0.0442 -0.0077 0.0364 charge_2 0.0127 0.0029 -0.0280 charge_3 0.0560 -0.0038 -0.0142 charge_4 -0.0319 0.0364 0.0116 charge_5 0.0000 0.0000 0.0000 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other 1.4675 1.6043 1.4596 unweighted_spectral_entropy -0.6540 -0.5893 -0.5083 delta_RT_loess 0.5531 0.1940 0.5050 m0 Found 4197 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 5868 target PSMs and 1529 decoy PSMs. Calculating q values. Final list yields 4199 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 15.4908 cpu seconds or 5 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0000_2] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatD_0000_2_percolator_target_psms.tsv --decoy-results-psms CatD_0000_2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatD_0000_2_edited.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 09:42:23 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll (lukall@u.washington.edu) in the Department of Genome Sciences at the University of Washington. Issued command: /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatD_0000_2_percolator_target_psms.tsv --decoy-results-psms CatD_0000_2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatD_0000_2_edited.pin Started Mon Sep 16 18:17:30 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile CatD_0000_2_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other unweighted_spectral_entropy delta_RT_loess Found 5311 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 4445 positives and 866 negatives, size ratio=5.13279 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 28 as initial direction. Could separate 2181 training set positives with q<0.01 in that direction. Split 2: Selected feature 28 as initial direction. Could separate 2220 training set positives with q<0.01 in that direction. Split 3: Selected feature 28 as initial direction. Could separate 2182 training set positives with q<0.01 in that direction. Found 3285 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 2.4495 cpu seconds or 0 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 3525 PSMs with q<0.01 Iteration 2: Estimated 3543 PSMs with q<0.01 Iteration 3: Estimated 3546 PSMs with q<0.01 Iteration 4: Estimated 3550 PSMs with q<0.01 Iteration 5: Estimated 3552 PSMs with q<0.01 Iteration 6: Estimated 3552 PSMs with q<0.01 Iteration 7: Estimated 3554 PSMs with q<0.01 Iteration 8: Estimated 3555 PSMs with q<0.01 Iteration 9: Estimated 3555 PSMs with q<0.01 Iteration 10: Estimated 3555 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName 0.0000 0.0000 0.0000 rank -0.1218 -0.1603 -0.2246 abs_ppm 0.0277 0.0527 0.0504 isotope_errors -1.1268 -1.0466 -1.1672 log10_evalue -0.0508 -0.0923 -0.0693 hyperscore 0.4035 0.6241 0.5176 delta_hyperscore -0.0485 -0.2006 -0.1204 matched_ion_num -0.4419 -0.4654 -0.6621 complementary_ions -0.2417 0.0051 -0.2637 ion_series 0.0266 0.0327 -0.0988 weighted_average_abs_fragment_ppm 0.0467 -0.0706 -0.0116 length_7 0.0763 0.3097 0.0669 length_8 -0.0530 -0.1306 -0.0391 length_9_30 -0.0595 -0.0665 0.0051 length_31 0.0000 0.0000 0.0000 ntt 0.0000 0.0000 0.0000 nmc 0.0000 0.0000 0.0000 charge_1 -0.1217 -0.1623 -0.1559 charge_2 0.0201 0.0792 0.0793 charge_3 0.1505 0.1285 0.0781 charge_4 -0.0678 -0.1035 0.0793 charge_5 -0.0119 -0.0132 -0.0121 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other 1.3169 1.4051 1.3729 unweighted_spectral_entropy -0.5306 -0.6664 -0.5999 delta_RT_loess 0.8658 0.9583 0.8834 m0 Found 3531 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 4445 target PSMs and 866 decoy PSMs. Calculating q values. Final list yields 3532 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 29.8867 cpu seconds or 21 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_2] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatB_0060_2_percolator_target_psms.tsv --decoy-results-psms CatB_0060_2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatB_0060_2_edited.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 09:42:23 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll (lukall@u.washington.edu) in the Department of Genome Sciences at the University of Washington. Issued command: /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatB_0060_2_percolator_target_psms.tsv --decoy-results-psms CatB_0060_2_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatB_0060_2_edited.pin Started Mon Sep 16 18:17:51 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile CatB_0060_2_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other unweighted_spectral_entropy delta_RT_loess Found 6389 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 5327 positives and 1062 negatives, size ratio=5.01601 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 28 as initial direction. Could separate 2658 training set positives with q<0.01 in that direction. Split 2: Selected feature 28 as initial direction. Could separate 2584 training set positives with q<0.01 in that direction. Split 3: Selected feature 28 as initial direction. Could separate 2602 training set positives with q<0.01 in that direction. Found 3873 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 3.2616 cpu seconds or 0 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 4126 PSMs with q<0.01 Iteration 2: Estimated 4161 PSMs with q<0.01 Iteration 3: Estimated 4164 PSMs with q<0.01 Iteration 4: Estimated 4174 PSMs with q<0.01 Iteration 5: Estimated 4173 PSMs with q<0.01 Iteration 6: Estimated 4178 PSMs with q<0.01 Iteration 7: Estimated 4184 PSMs with q<0.01 Iteration 8: Estimated 4181 PSMs with q<0.01 Iteration 9: Estimated 4186 PSMs with q<0.01 Iteration 10: Estimated 4189 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName 0.0000 0.0000 0.0000 rank -0.1428 -0.1496 -0.0571 abs_ppm -0.0642 -0.0306 -0.1634 isotope_errors -1.4169 -1.1028 -1.1985 log10_evalue -0.8027 -0.0699 -0.0366 hyperscore 0.7801 0.3671 0.4348 delta_hyperscore 0.6533 0.3828 0.3125 matched_ion_num -0.8253 -0.6634 -0.8286 complementary_ions -0.3247 -0.0822 -0.3071 ion_series -0.0306 -0.0101 -0.0168 weighted_average_abs_fragment_ppm -0.0263 -0.0622 -0.0237 length_7 0.0292 0.1556 0.0339 length_8 0.0184 -0.0488 0.0094 length_9_30 -0.0569 -0.0537 -0.0465 length_31 0.0000 0.0000 0.0000 ntt 0.0000 0.0000 0.0000 nmc 0.0000 0.0000 0.0000 charge_1 -0.1519 0.0036 -0.1185 charge_2 0.0997 0.0009 0.0730 charge_3 0.0537 -0.0030 0.0611 charge_4 0.0557 -0.0149 -0.0085 charge_5 0.0000 0.0000 0.0000 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other 1.5548 1.0614 1.3287 unweighted_spectral_entropy -0.1941 -0.4898 -0.2090 delta_RT_loess 0.9911 0.9344 0.8102 m0 Found 4099 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 5327 target PSMs and 1062 decoy PSMs. Calculating q values. Final list yields 4105 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 17.3350 cpu seconds or 8 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_3] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatA_0090_3_percolator_target_psms.tsv --decoy-results-psms CatA_0090_3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatA_0090_3_edited.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 09:42:23 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll (lukall@u.washington.edu) in the Department of Genome Sciences at the University of Washington. Issued command: /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatA_0090_3_percolator_target_psms.tsv --decoy-results-psms CatA_0090_3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatA_0090_3_edited.pin Started Mon Sep 16 18:17:59 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile CatA_0090_3_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other unweighted_spectral_entropy delta_RT_loess Found 4983 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 4585 positives and 398 negatives, size ratio=11.5201 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 28 as initial direction. Could separate 2623 training set positives with q<0.01 in that direction. Split 2: Selected feature 28 as initial direction. Could separate 2657 training set positives with q<0.01 in that direction. Split 3: Selected feature 28 as initial direction. Could separate 2749 training set positives with q<0.01 in that direction. Found 4003 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 2.1404 cpu seconds or 0 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 4200 PSMs with q<0.01 Iteration 2: Estimated 4208 PSMs with q<0.01 Iteration 3: Estimated 4211 PSMs with q<0.01 Iteration 4: Estimated 4212 PSMs with q<0.01 Iteration 5: Estimated 4211 PSMs with q<0.01 Iteration 6: Estimated 4213 PSMs with q<0.01 Iteration 7: Estimated 4212 PSMs with q<0.01 Iteration 8: Estimated 4214 PSMs with q<0.01 Iteration 9: Estimated 4214 PSMs with q<0.01 Iteration 10: Estimated 4215 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName 0.0000 0.0000 0.0000 rank -0.1951 -0.1071 -0.1388 abs_ppm -0.0707 0.0245 -0.2061 isotope_errors -0.9793 -1.0035 -1.0307 log10_evalue 0.8346 0.2594 0.1851 hyperscore 0.2824 0.4602 -0.0008 delta_hyperscore -0.9202 -0.3594 -0.7940 matched_ion_num -0.5444 -0.7661 -0.6219 complementary_ions 0.2221 0.0025 0.5087 ion_series -0.0616 -0.0431 -0.1541 weighted_average_abs_fragment_ppm -0.0497 -0.0393 0.3038 length_7 0.1434 0.0898 -0.0366 length_8 -0.0505 -0.0238 -0.2022 length_9_30 -0.0374 -0.0335 0.0046 length_31 0.0000 0.0000 0.0000 ntt 0.0000 0.0000 0.0000 nmc 0.0000 0.0000 0.0000 charge_1 -0.2036 -0.1113 -0.0823 charge_2 0.1293 0.0644 -0.0072 charge_3 0.0816 0.0437 0.1160 charge_4 0.0260 0.0674 0.0070 charge_5 -0.0216 -0.0193 -0.0235 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other 0.6776 0.8165 1.0277 unweighted_spectral_entropy -0.4918 -0.3540 -0.3994 delta_RT_loess 1.5249 1.3651 1.6601 m0 Found 4152 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 4585 target PSMs and 398 decoy PSMs. Calculating q values. Final list yields 4158 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 38.0704 cpu seconds or 23 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_3] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatD_0015_3_percolator_target_psms.tsv --decoy-results-psms CatD_0015_3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatD_0015_3_edited.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 09:42:23 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll (lukall@u.washington.edu) in the Department of Genome Sciences at the University of Washington. Issued command: /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatD_0015_3_percolator_target_psms.tsv --decoy-results-psms CatD_0015_3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatD_0015_3_edited.pin Started Mon Sep 16 18:18:22 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile CatD_0015_3_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other unweighted_spectral_entropy delta_RT_loess Found 5251 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 4273 positives and 978 negatives, size ratio=4.36912 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 28 as initial direction. Could separate 2060 training set positives with q<0.01 in that direction. Split 2: Selected feature 28 as initial direction. Could separate 2080 training set positives with q<0.01 in that direction. Split 3: Selected feature 28 as initial direction. Could separate 2024 training set positives with q<0.01 in that direction. Found 3034 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 2.1611 cpu seconds or 0 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 3225 PSMs with q<0.01 Iteration 2: Estimated 3249 PSMs with q<0.01 Iteration 3: Estimated 3256 PSMs with q<0.01 Iteration 4: Estimated 3253 PSMs with q<0.01 Iteration 5: Estimated 3254 PSMs with q<0.01 Iteration 6: Estimated 3255 PSMs with q<0.01 Iteration 7: Estimated 3256 PSMs with q<0.01 Iteration 8: Estimated 3256 PSMs with q<0.01 Iteration 9: Estimated 3256 PSMs with q<0.01 Iteration 10: Estimated 3256 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName 0.0000 0.0000 0.0000 rank -0.3581 -0.0673 -0.3929 abs_ppm -0.1615 -0.2113 -0.1575 isotope_errors -0.6161 -1.0843 -0.6206 log10_evalue 0.3478 -0.0737 0.3083 hyperscore 0.5335 0.4025 0.9660 delta_hyperscore 0.2973 0.3175 0.0316 matched_ion_num -0.5542 -0.9478 -0.4759 complementary_ions -0.0741 -0.2775 0.0133 ion_series -0.1850 -0.2533 -0.3417 weighted_average_abs_fragment_ppm 0.0557 -0.0616 -0.0381 length_7 0.0230 -0.1023 -0.1063 length_8 -0.0388 0.1235 0.1167 length_9_30 -0.0512 -0.0398 -0.0625 length_31 0.0000 0.0000 0.0000 ntt 0.0000 0.0000 0.0000 nmc 0.0000 0.0000 0.0000 charge_1 -0.0690 -0.0523 -0.0743 charge_2 -0.0006 0.0219 0.1267 charge_3 0.1020 0.0372 -0.0982 charge_4 -0.0019 0.0266 0.0663 charge_5 -0.0117 -0.0091 -0.0143 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other 1.2353 1.7503 1.6486 unweighted_spectral_entropy -0.1897 -0.6034 -0.4333 delta_RT_loess 0.8491 0.6597 1.0369 m0 Found 3185 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 4273 target PSMs and 978 decoy PSMs. Calculating q values. Final list yields 3192 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 62.3554 cpu seconds or 12 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_3] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatC_0030_3_percolator_target_psms.tsv --decoy-results-psms CatC_0030_3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatC_0030_3_edited.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 09:42:23 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll (lukall@u.washington.edu) in the Department of Genome Sciences at the University of Washington. Issued command: /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatC_0030_3_percolator_target_psms.tsv --decoy-results-psms CatC_0030_3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatC_0030_3_edited.pin Started Mon Sep 16 18:18:34 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile CatC_0030_3_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other unweighted_spectral_entropy delta_RT_loess Found 7450 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 6503 positives and 947 negatives, size ratio=6.86695 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 28 as initial direction. Could separate 3477 training set positives with q<0.01 in that direction. Split 2: Selected feature 28 as initial direction. Could separate 3518 training set positives with q<0.01 in that direction. Split 3: Selected feature 28 as initial direction. Could separate 3494 training set positives with q<0.01 in that direction. Found 5217 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 2.9702 cpu seconds or 0 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 5529 PSMs with q<0.01 Iteration 2: Estimated 5550 PSMs with q<0.01 Iteration 3: Estimated 5554 PSMs with q<0.01 Iteration 4: Estimated 5553 PSMs with q<0.01 Iteration 5: Estimated 5554 PSMs with q<0.01 Iteration 6: Estimated 5555 PSMs with q<0.01 Iteration 7: Estimated 5554 PSMs with q<0.01 Iteration 8: Estimated 5554 PSMs with q<0.01 Iteration 9: Estimated 5555 PSMs with q<0.01 Iteration 10: Estimated 5554 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName 0.0000 0.0000 0.0000 rank -0.1579 -0.1284 -0.2755 abs_ppm -0.0974 -0.0856 -0.1162 isotope_errors -1.2931 -1.3902 -0.9704 log10_evalue -0.2636 -0.2727 -0.0879 hyperscore 0.2330 0.2942 0.1847 delta_hyperscore 0.2361 0.1973 0.5176 matched_ion_num -0.7286 -0.8008 -0.9047 complementary_ions -0.0710 -0.3410 -0.1035 ion_series -0.1486 -0.0914 -0.2041 weighted_average_abs_fragment_ppm 0.0038 0.0569 -0.0122 length_7 0.0120 -0.0184 -0.0266 length_8 0.0231 0.0034 0.0642 length_9_30 -0.0725 -0.0532 -0.0850 length_31 0.0000 0.0000 0.0000 ntt 0.0000 0.0000 0.0000 nmc 0.0000 0.0000 0.0000 charge_1 -0.0936 -0.0922 -0.0924 charge_2 0.0223 0.0793 -0.0180 charge_3 0.0667 -0.0093 0.1215 charge_4 0.1256 0.0954 0.1267 charge_5 -0.0193 -0.0142 -0.0227 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other 1.0655 1.2762 1.2419 unweighted_spectral_entropy -0.4523 -0.3477 -0.4606 delta_RT_loess 1.1797 0.8663 1.3844 m0 Found 5515 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 6503 target PSMs and 947 decoy PSMs. Calculating q values. Final list yields 5516 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 17.9225 cpu seconds or 5 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_3] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatA_0030_3_percolator_target_psms.tsv --decoy-results-psms CatA_0030_3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatA_0030_3_edited.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 09:42:23 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll (lukall@u.washington.edu) in the Department of Genome Sciences at the University of Washington. Issued command: /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatA_0030_3_percolator_target_psms.tsv --decoy-results-psms CatA_0030_3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatA_0030_3_edited.pin Started Mon Sep 16 18:18:39 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile CatA_0030_3_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other unweighted_spectral_entropy delta_RT_loess Found 5083 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 4647 positives and 436 negatives, size ratio=10.6583 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 28 as initial direction. Could separate 2678 training set positives with q<0.01 in that direction. Split 2: Selected feature 28 as initial direction. Could separate 2668 training set positives with q<0.01 in that direction. Split 3: Selected feature 28 as initial direction. Could separate 2660 training set positives with q<0.01 in that direction. Found 3997 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 2.3814 cpu seconds or 0 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 4218 PSMs with q<0.01 Iteration 2: Estimated 4246 PSMs with q<0.01 Iteration 3: Estimated 4247 PSMs with q<0.01 Iteration 4: Estimated 4248 PSMs with q<0.01 Iteration 5: Estimated 4247 PSMs with q<0.01 Iteration 6: Estimated 4246 PSMs with q<0.01 Iteration 7: Estimated 4246 PSMs with q<0.01 Iteration 8: Estimated 4246 PSMs with q<0.01 Iteration 9: Estimated 4246 PSMs with q<0.01 Iteration 10: Estimated 4246 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName 0.0000 0.0000 0.0000 rank -0.1309 -0.1519 -0.2727 abs_ppm -0.0609 -0.0624 -0.0980 isotope_errors -0.6000 -0.7741 -0.9590 log10_evalue 0.9488 0.1635 0.2495 hyperscore -0.1216 -0.0154 -0.2261 delta_hyperscore -0.1490 0.0455 -0.0442 matched_ion_num -0.8534 -0.4844 -0.7734 complementary_ions -0.6307 -0.5267 -0.1201 ion_series -0.0172 0.0305 -0.0023 weighted_average_abs_fragment_ppm 0.0355 -0.0637 0.0056 length_7 -0.0375 0.2033 -0.0474 length_8 0.0103 -0.0906 0.0384 length_9_30 -0.0386 -0.0315 -0.0408 length_31 0.0000 0.0000 0.0000 ntt 0.0000 0.0000 0.0000 nmc 0.0000 0.0000 0.0000 charge_1 -0.1640 -0.1680 -0.1954 charge_2 0.0029 0.0259 0.0573 charge_3 0.1578 0.1337 0.1455 charge_4 0.2028 0.1940 0.0904 charge_5 0.0000 0.0000 0.0000 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other 1.2481 0.8906 0.9901 unweighted_spectral_entropy -0.5798 -0.5385 -0.6047 delta_RT_loess 1.2304 1.0027 1.2996 m0 Found 4236 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 4647 target PSMs and 436 decoy PSMs. Calculating q values. Final list yields 4241 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 23.1634 cpu seconds or 12 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_3] /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatB_0015_3_percolator_target_psms.tsv --decoy-results-psms CatB_0015_3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatB_0015_3_edited.pin Protein decoy-prefix used is rev_ All files have been read Percolator version 3.06.4, Build Date Dec 4 2023 09:42:23 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll (lukall@u.washington.edu) in the Department of Genome Sciences at the University of Washington. Issued command: /home/nanopore-catalyst/fragpipe/tools/percolator_3_6_4/linux/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 23 --results-psms CatB_0015_3_percolator_target_psms.tsv --decoy-results-psms CatB_0015_3_percolator_decoy_psms.tsv --protein-decoy-pattern rev_ CatB_0015_3_edited.pin Started Mon Sep 16 18:18:51 2024 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile CatB_0015_3_edited.pin Features: rank abs_ppm isotope_errors log10_evalue hyperscore delta_hyperscore matched_ion_num complementary_ions ion_series weighted_average_abs_fragment_ppm length_7 length_8 length_9_30 length_31 ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other unweighted_spectral_entropy delta_RT_loess Found 7214 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 5758 positives and 1456 negatives, size ratio=3.95467 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 28 as initial direction. Could separate 2657 training set positives with q<0.01 in that direction. Split 2: Selected feature 28 as initial direction. Could separate 2643 training set positives with q<0.01 in that direction. Split 3: Selected feature 28 as initial direction. Could separate 2706 training set positives with q<0.01 in that direction. Found 3990 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 9.6778 cpu seconds or 1 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 4265 PSMs with q<0.01 Iteration 2: Estimated 4325 PSMs with q<0.01 Iteration 3: Estimated 4332 PSMs with q<0.01 Iteration 4: Estimated 4340 PSMs with q<0.01 Iteration 5: Estimated 4342 PSMs with q<0.01 Iteration 6: Estimated 4341 PSMs with q<0.01 Iteration 7: Estimated 4341 PSMs with q<0.01 Iteration 8: Estimated 4340 PSMs with q<0.01 Iteration 9: Estimated 4341 PSMs with q<0.01 Iteration 10: Estimated 4339 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName 0.0000 0.0000 0.0000 rank -0.3049 -0.2608 -0.2372 abs_ppm -0.1435 0.0061 -0.0799 isotope_errors -1.9392 -0.8925 -1.3801 log10_evalue -1.3312 -0.1664 -0.4066 hyperscore 0.4306 0.5106 0.4272 delta_hyperscore 0.6010 0.0343 0.6357 matched_ion_num -0.7972 -0.5337 -0.8990 complementary_ions -0.6680 -0.3663 -0.6758 ion_series -0.1432 -0.0517 0.0083 weighted_average_abs_fragment_ppm -0.0608 -0.0582 -0.0185 length_7 0.0252 0.0828 0.1350 length_8 0.0269 -0.0044 -0.0700 length_9_30 -0.0148 -0.0254 -0.0060 length_31 0.0000 0.0000 0.0000 ntt 0.0000 0.0000 0.0000 nmc 0.0000 0.0000 0.0000 charge_1 -0.0788 -0.1132 -0.1166 charge_2 -0.0158 0.0524 0.0335 charge_3 0.1348 0.1006 0.1303 charge_4 0.0257 -0.0458 -0.0291 charge_5 -0.0039 -0.0068 -0.0046 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other 1.8283 1.5133 1.2275 unweighted_spectral_entropy -0.6271 -0.6328 -0.3910 delta_RT_loess 0.1935 0.3319 0.2273 m0 Found 4271 test set PSMs with q<0.01. Selected best-scoring PSM per file+scan+expMass (target-decoy competition): 5758 target PSMs and 1456 decoy PSMs. Calculating q values. Final list yields 4275 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 19.1811 cpu seconds or 5 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_3] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatC_0090_3.pin CatC_0090_3 CatC_0090_3_percolator_target_psms.tsv CatC_0090_3_percolator_decoy_psms.tsv interact-CatC_0090_3 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0090_3_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_3/CatC_0090_3_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_3/CatC_0090_3_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_4] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatA_0030_4.pin CatA_0030_4 CatA_0030_4_percolator_target_psms.tsv CatA_0030_4_percolator_decoy_psms.tsv interact-CatA_0030_4 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0030_4_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_4/CatA_0030_4_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_4/CatA_0030_4_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_2] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatC_0030_2.pin CatC_0030_2 CatC_0030_2_percolator_target_psms.tsv CatC_0030_2_percolator_decoy_psms.tsv interact-CatC_0030_2 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0030_2_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_2/CatC_0030_2_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_2/CatC_0030_2_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_1] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatB_0015_1.pin CatB_0015_1 CatB_0015_1_percolator_target_psms.tsv CatB_0015_1_percolator_decoy_psms.tsv interact-CatB_0015_1 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0015_1_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_1/CatB_0015_1_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_1/CatB_0015_1_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_4] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatC_0030_4.pin CatC_0030_4 CatC_0030_4_percolator_target_psms.tsv CatC_0030_4_percolator_decoy_psms.tsv interact-CatC_0030_4 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0030_4_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_4/CatC_0030_4_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_4/CatC_0030_4_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_2] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatA_0000_2.pin CatA_0000_2 CatA_0000_2_percolator_target_psms.tsv CatA_0000_2_percolator_decoy_psms.tsv interact-CatA_0000_2 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0000_2_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_2/CatA_0000_2_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_2/CatA_0000_2_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_1] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatC_0090_1.pin CatC_0090_1 CatC_0090_1_percolator_target_psms.tsv CatC_0090_1_percolator_decoy_psms.tsv interact-CatC_0090_1 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0090_1_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_1/CatC_0090_1_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_1/CatC_0090_1_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_1] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatB_0060_1.pin CatB_0060_1 CatB_0060_1_percolator_target_psms.tsv CatB_0060_1_percolator_decoy_psms.tsv interact-CatB_0060_1 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0060_1_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_1/CatB_0060_1_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_1/CatB_0060_1_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_1] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatD_0015_1.pin CatD_0015_1 CatD_0015_1_percolator_target_psms.tsv CatD_0015_1_percolator_decoy_psms.tsv interact-CatD_0015_1 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0015_1_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_1/CatD_0015_1_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_1/CatD_0015_1_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_1] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatA_0030_1.pin CatA_0030_1 CatA_0030_1_percolator_target_psms.tsv CatA_0030_1_percolator_decoy_psms.tsv interact-CatA_0030_1 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0030_1_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_1/CatA_0030_1_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_1/CatA_0030_1_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_3] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatB_0000_3.pin CatB_0000_3 CatB_0000_3_percolator_target_psms.tsv CatB_0000_3_percolator_decoy_psms.tsv interact-CatB_0000_3 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0000_3_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_3/CatB_0000_3_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_3/CatB_0000_3_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_2] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatA_0090_2.pin CatA_0090_2 CatA_0090_2_percolator_target_psms.tsv CatA_0090_2_percolator_decoy_psms.tsv interact-CatA_0090_2 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0090_2_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_2/CatA_0090_2_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_2/CatA_0090_2_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_3] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatB_0060_3.pin CatB_0060_3 CatB_0060_3_percolator_target_psms.tsv CatB_0060_3_percolator_decoy_psms.tsv interact-CatB_0060_3 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0060_3_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_3/CatB_0060_3_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_3/CatB_0060_3_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_4] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatD_0015_4.pin CatD_0015_4 CatD_0015_4_percolator_target_psms.tsv CatD_0015_4_percolator_decoy_psms.tsv interact-CatD_0015_4 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0015_4_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_4/CatD_0015_4_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_4/CatD_0015_4_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_2] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatA_0030_2.pin CatA_0030_2 CatA_0030_2_percolator_target_psms.tsv CatA_0030_2_percolator_decoy_psms.tsv interact-CatA_0030_2 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0030_2_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_2/CatA_0030_2_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_2/CatA_0030_2_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_2] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatD_0015_2.pin CatD_0015_2 CatD_0015_2_percolator_target_psms.tsv CatD_0015_2_percolator_decoy_psms.tsv interact-CatD_0015_2 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0015_2_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_2/CatD_0015_2_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_2/CatD_0015_2_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_3] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatA_0000_3.pin CatA_0000_3 CatA_0000_3_percolator_target_psms.tsv CatA_0000_3_percolator_decoy_psms.tsv interact-CatA_0000_3 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0000_3_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_3/CatA_0000_3_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_3/CatA_0000_3_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_2] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatC_0090_2.pin CatC_0090_2 CatC_0090_2_percolator_target_psms.tsv CatC_0090_2_percolator_decoy_psms.tsv interact-CatC_0090_2 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0090_2_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_2/CatC_0090_2_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_2/CatC_0090_2_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_3] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatC_0000_3.pin CatC_0000_3 CatC_0000_3_percolator_target_psms.tsv CatC_0000_3_percolator_decoy_psms.tsv interact-CatC_0000_3 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0000_3_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_3/CatC_0000_3_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_3/CatC_0000_3_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatA_0000_1.pin CatA_0000_1 CatA_0000_1_percolator_target_psms.tsv CatA_0000_1_percolator_decoy_psms.tsv interact-CatA_0000_1 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0000_1_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1/CatA_0000_1_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1/CatA_0000_1_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_4] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatC_0000_4.pin CatC_0000_4 CatC_0000_4_percolator_target_psms.tsv CatC_0000_4_percolator_decoy_psms.tsv interact-CatC_0000_4 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0000_4_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_4/CatC_0000_4_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_4/CatC_0000_4_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_2] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatB_0015_2.pin CatB_0015_2 CatB_0015_2_percolator_target_psms.tsv CatB_0015_2_percolator_decoy_psms.tsv interact-CatB_0015_2 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0015_2_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_2/CatB_0015_2_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_2/CatB_0015_2_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_4] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatB_0015_4.pin CatB_0015_4 CatB_0015_4_percolator_target_psms.tsv CatB_0015_4_percolator_decoy_psms.tsv interact-CatB_0015_4 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0015_4_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_4/CatB_0015_4_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_4/CatB_0015_4_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_1] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatB_0000_1.pin CatB_0000_1 CatB_0000_1_percolator_target_psms.tsv CatB_0000_1_percolator_decoy_psms.tsv interact-CatB_0000_1 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0000_1_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_1/CatB_0000_1_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_1/CatB_0000_1_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_1] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatA_0090_1.pin CatA_0090_1 CatA_0090_1_percolator_target_psms.tsv CatA_0090_1_percolator_decoy_psms.tsv interact-CatA_0090_1 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0090_1_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_1/CatA_0090_1_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_1/CatA_0090_1_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_4] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatA_0090_4.pin CatA_0090_4 CatA_0090_4_percolator_target_psms.tsv CatA_0090_4_percolator_decoy_psms.tsv interact-CatA_0090_4 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0090_4_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_4/CatA_0090_4_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_4/CatA_0090_4_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_1] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatC_0000_1.pin CatC_0000_1 CatC_0000_1_percolator_target_psms.tsv CatC_0000_1_percolator_decoy_psms.tsv interact-CatC_0000_1 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0000_1_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_1/CatC_0000_1_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_1/CatC_0000_1_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_1] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatC_0030_1.pin CatC_0030_1 CatC_0030_1_percolator_target_psms.tsv CatC_0030_1_percolator_decoy_psms.tsv interact-CatC_0030_1 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0030_1_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_1/CatC_0030_1_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_1/CatC_0030_1_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_4] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatC_0090_4.pin CatC_0090_4 CatC_0090_4_percolator_target_psms.tsv CatC_0090_4_percolator_decoy_psms.tsv interact-CatC_0090_4 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0090_4_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_4/CatC_0090_4_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_4/CatC_0090_4_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_2] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatC_0000_2.pin CatC_0000_2 CatC_0000_2_percolator_target_psms.tsv CatC_0000_2_percolator_decoy_psms.tsv interact-CatC_0000_2 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0000_2_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_2/CatC_0000_2_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_2/CatC_0000_2_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0000_1] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatD_0000_1.pin CatD_0000_1 CatD_0000_1_percolator_target_psms.tsv CatD_0000_1_percolator_decoy_psms.tsv interact-CatD_0000_1 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0000_1_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0000_1/CatD_0000_1_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0000_1/CatD_0000_1_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_4] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatB_0060_4.pin CatB_0060_4 CatB_0060_4_percolator_target_psms.tsv CatB_0060_4_percolator_decoy_psms.tsv interact-CatB_0060_4 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0060_4_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_4/CatB_0060_4_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_4/CatB_0060_4_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_2] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatB_0000_2.pin CatB_0000_2 CatB_0000_2_percolator_target_psms.tsv CatB_0000_2_percolator_decoy_psms.tsv interact-CatB_0000_2 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0000_2_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_2/CatB_0000_2_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_2/CatB_0000_2_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_4] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatA_0000_4.pin CatA_0000_4 CatA_0000_4_percolator_target_psms.tsv CatA_0000_4_percolator_decoy_psms.tsv interact-CatA_0000_4 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0000_4_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_4/CatA_0000_4_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_4/CatA_0000_4_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_4] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatB_0000_4.pin CatB_0000_4 CatB_0000_4_percolator_target_psms.tsv CatB_0000_4_percolator_decoy_psms.tsv interact-CatB_0000_4 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0000_4_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_4/CatB_0000_4_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_4/CatB_0000_4_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0000_2] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatD_0000_2.pin CatD_0000_2 CatD_0000_2_percolator_target_psms.tsv CatD_0000_2_percolator_decoy_psms.tsv interact-CatD_0000_2 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0000_2_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0000_2/CatD_0000_2_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0000_2/CatD_0000_2_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_2] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatB_0060_2.pin CatB_0060_2 CatB_0060_2_percolator_target_psms.tsv CatB_0060_2_percolator_decoy_psms.tsv interact-CatB_0060_2 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0060_2_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_2/CatB_0060_2_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_2/CatB_0060_2_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_3] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatA_0090_3.pin CatA_0090_3 CatA_0090_3_percolator_target_psms.tsv CatA_0090_3_percolator_decoy_psms.tsv interact-CatA_0090_3 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0090_3_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_3/CatA_0090_3_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_3/CatA_0090_3_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_3] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatD_0015_3.pin CatD_0015_3 CatD_0015_3_percolator_target_psms.tsv CatD_0015_3_percolator_decoy_psms.tsv interact-CatD_0015_3 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0015_3_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_3/CatD_0015_3_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_3/CatD_0015_3_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_3] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatC_0030_3.pin CatC_0030_3 CatC_0030_3_percolator_target_psms.tsv CatC_0030_3_percolator_decoy_psms.tsv interact-CatC_0030_3 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0030_3_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_3/CatC_0030_3_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_3/CatC_0030_3_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_3] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatA_0030_3.pin CatA_0030_3 CatA_0030_3_percolator_target_psms.tsv CatA_0030_3_percolator_decoy_psms.tsv interact-CatA_0030_3 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0030_3_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_3/CatA_0030_3_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_3/CatA_0030_3_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Convert to pepxml [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_3] java -cp /home/nanopore-catalyst/fragpipe/lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML CatB_0015_3.pin CatB_0015_3 CatB_0015_3_percolator_target_psms.tsv CatB_0015_3_percolator_decoy_psms.tsv interact-CatB_0015_3 DDA 0.5 /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0015_3_uncalibrated.mzML Process 'Percolator: Convert to pepxml' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_3/CatB_0015_3_percolator_target_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 Percolator: Delete temp java -cp /home/nanopore-catalyst/fragpipe/lib/fragpipe-21.1.jar com.github.chhh.utils.FileDelete /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_3/CatB_0015_3_percolator_decoy_psms.tsv Process 'Percolator: Delete temp' finished, exit code: 0 ProteinProphet [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher proteinprophet --maxppmdiff 2000000 --output combined /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/filelist_proteinprophet.txt time="18:19:32" level=info msg="Executing ProteinProphet v5.1.0" ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v6.0.0-rc15 Noctilucent, Build 202105021430-exported (Linux-x86_64)) (no FPKM) (no groups) (using degen pep info) Reading in /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1/interact-CatA_0000_1.pep.xml... ...read in 0 1+, 1377 2+, 2314 3+, 710 4+, 27 5+, 0 6+, 0 7+ spectra with min prob 0.05 Reading in /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_2/interact-CatA_0000_2.pep.xml... ...read in 0 1+, 1309 2+, 2184 3+, 732 4+, 25 5+, 0 6+, 0 7+ spectra with min prob 0.05 Reading in /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_3/interact-CatA_0000_3.pep.xml... ...read in 0 1+, 1390 2+, 2322 3+, 687 4+, 23 5+, 0 6+, 0 7+ spectra with min prob 0.05 Reading in /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_4/interact-CatA_0000_4.pep.xml... ...read in 0 1+, 1370 2+, 2340 3+, 740 4+, 31 5+, 0 6+, 0 7+ spectra with min prob 0.05 Reading in /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_1/interact-CatA_0030_1.pep.xml... ...read in 0 1+, 1363 2+, 2186 3+, 682 4+, 23 5+, 0 6+, 0 7+ spectra with min prob 0.05 Reading in /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_2/interact-CatA_0030_2.pep.xml... ...read in 0 1+, 1301 2+, 2102 3+, 682 4+, 19 5+, 0 6+, 0 7+ spectra with min prob 0.05 Reading in /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_3/interact-CatA_0030_3.pep.xml... ...read in 0 1+, 1334 2+, 2186 3+, 751 4+, 25 5+, 0 6+, 0 7+ spectra with min prob 0.05 Reading in /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_4/interact-CatA_0030_4.pep.xml... ...read in 0 1+, 1538 2+, 2380 3+, 802 4+, 26 5+, 0 6+, 0 7+ spectra with min prob 0.05 Reading in /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_1/interact-CatA_0090_1.pep.xml... ...read in 0 1+, 1405 2+, 2149 3+, 748 4+, 19 5+, 0 6+, 0 7+ spectra with min prob 0.05 Reading in /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_2/interact-CatA_0090_2.pep.xml... ...read in 0 1+, 1375 2+, 2120 3+, 718 4+, 15 5+, 0 6+, 0 7+ spectra with min prob 0.05 Reading in /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_3/interact-CatA_0090_3.pep.xml... ...read in 0 1+, 1461 2+, 2104 3+, 697 4+, 20 5+, 0 6+, 0 7+ spectra with min prob 0.05 Reading in /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_4/interact-CatA_0090_4.pep.xml... ...read in 0 1+, 1407 2+, 2115 3+, 688 4+, 21 5+, 0 6+, 0 7+ spectra with min prob 0.05 Reading in /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_1/interact-CatB_0000_1.pep.xml... ...read in 0 1+, 1433 2+, 1873 3+, 406 4+, 17 5+, 0 6+, 0 7+ spectra with min prob 0.05 Reading in /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_2/interact-CatB_0000_2.pep.xml... ...read in 0 1+, 1479 2+, 2018 3+, 405 4+, 10 5+, 0 6+, 0 7+ spectra with min prob 0.05 Reading in /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_3/interact-CatB_0000_3.pep.xml... ...read in 0 1+, 1733 2+, 2123 3+, 492 4+, 17 5+, 0 6+, 0 7+ spectra with min prob 0.05 Reading in /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_4/interact-CatB_0000_4.pep.xml... ...read in 0 1+, 1786 2+, 2120 3+, 465 4+, 21 5+, 0 6+, 0 7+ spectra with min prob 0.05 Reading in /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_1/interact-CatB_0015_1.pep.xml... ...read in 0 1+, 1635 2+, 2066 3+, 520 4+, 21 5+, 0 6+, 0 7+ spectra with min prob 0.05 Reading in /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_2/interact-CatB_0015_2.pep.xml... ...read in 0 1+, 1740 2+, 2039 3+, 369 4+, 12 5+, 0 6+, 0 7+ spectra with min prob 0.05 Reading in /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_3/interact-CatB_0015_3.pep.xml... ...read in 0 1+, 1732 2+, 2207 3+, 529 4+, 18 5+, 0 6+, 0 7+ spectra with min prob 0.05 Reading in /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_4/interact-CatB_0015_4.pep.xml... ...read in 0 1+, 1760 2+, 2242 3+, 534 4+, 21 5+, 0 6+, 0 7+ spectra with min prob 0.05 Reading in /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_1/interact-CatB_0060_1.pep.xml... ...read in 0 1+, 1627 2+, 2144 3+, 502 4+, 18 5+, 0 6+, 0 7+ spectra with min prob 0.05 Reading in /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_2/interact-CatB_0060_2.pep.xml... ...read in 0 1+, 1635 2+, 2143 3+, 538 4+, 18 5+, 0 6+, 0 7+ spectra with min prob 0.05 Reading in /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_3/interact-CatB_0060_3.pep.xml... ...read in 0 1+, 1750 2+, 2235 3+, 520 4+, 20 5+, 0 6+, 0 7+ spectra with min prob 0.05 Reading in /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_4/interact-CatB_0060_4.pep.xml... ...read in 0 1+, 1707 2+, 2192 3+, 503 4+, 13 5+, 0 6+, 0 7+ spectra with min prob 0.05 Reading in /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_1/interact-CatC_0000_1.pep.xml... ...read in 0 1+, 1864 2+, 2793 3+, 766 4+, 33 5+, 0 6+, 0 7+ spectra with min prob 0.05 Reading in /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_2/interact-CatC_0000_2.pep.xml... ...read in 0 1+, 1889 2+, 2889 3+, 867 4+, 30 5+, 0 6+, 0 7+ spectra with min prob 0.05 Reading in /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_3/interact-CatC_0000_3.pep.xml... ...read in 0 1+, 1840 2+, 2796 3+, 811 4+, 34 5+, 0 6+, 0 7+ spectra with min prob 0.05 Reading in /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_4/interact-CatC_0000_4.pep.xml... ...read in 0 1+, 1867 2+, 2828 3+, 887 4+, 32 5+, 0 6+, 0 7+ spectra with min prob 0.05 Reading in /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_1/interact-CatC_0030_1.pep.xml... ...read in 0 1+, 1859 2+, 2749 3+, 772 4+, 29 5+, 0 6+, 0 7+ spectra with min prob 0.05 Reading in /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_2/interact-CatC_0030_2.pep.xml... ...read in 0 1+, 1840 2+, 2771 3+, 821 4+, 31 5+, 0 6+, 0 7+ spectra with min prob 0.05 Reading in /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_3/interact-CatC_0030_3.pep.xml... ...read in 0 1+, 1936 2+, 2878 3+, 818 4+, 32 5+, 0 6+, 0 7+ spectra with min prob 0.05 Reading in /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_4/interact-CatC_0030_4.pep.xml... ...read in 0 1+, 1819 2+, 2787 3+, 832 4+, 36 5+, 0 6+, 0 7+ spectra with min prob 0.05 Reading in /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_1/interact-CatC_0090_1.pep.xml... ...read in 0 1+, 1834 2+, 2676 3+, 807 4+, 30 5+, 0 6+, 0 7+ spectra with min prob 0.05 Reading in /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_2/interact-CatC_0090_2.pep.xml... ...read in 0 1+, 1978 2+, 2789 3+, 807 4+, 33 5+, 0 6+, 0 7+ spectra with min prob 0.05 Reading in /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_3/interact-CatC_0090_3.pep.xml... ...read in 0 1+, 1935 2+, 2779 3+, 816 4+, 32 5+, 0 6+, 0 7+ spectra with min prob 0.05 Reading in /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_4/interact-CatC_0090_4.pep.xml... ...read in 0 1+, 2049 2+, 2898 3+, 826 4+, 29 5+, 0 6+, 0 7+ spectra with min prob 0.05 Reading in /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0000_1/interact-CatD_0000_1.pep.xml... WARNING: Trying to compute mass of non-residue: WARNING: Trying to compute mass of non-residue: WARNING: Trying to compute mass of non-residue: WARNING: Trying to compute mass of non-residue: WARNING: Trying to compute mass of non-residue: WARNING: Trying to compute mass of non-residue: WARNING: Trying to compute mass of non-residue: WARNING: Trying to compute mass of non-residue: WARNING: Trying to compute mass of non-residue: WARNING: Trying to compute mass of non-residue: WARNING: Trying to compute mass of non-residue: WARNING: Trying to compute mass of non-residue: ...read in 0 1+, 1309 2+, 1809 3+, 521 4+, 23 5+, 0 6+, 0 7+ spectra with min prob 0.05 Reading in /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0000_2/interact-CatD_0000_2.pep.xml... ...read in 0 1+, 1319 2+, 1813 3+, 510 4+, 17 5+, 0 6+, 0 7+ spectra with min prob 0.05 Reading in /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_1/interact-CatD_0015_1.pep.xml... ...read in 0 1+, 1439 2+, 1707 3+, 485 4+, 13 5+, 0 6+, 0 7+ spectra with min prob 0.05 Reading in /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_2/interact-CatD_0015_2.pep.xml... ...read in 0 1+, 1113 2+, 1556 3+, 428 4+, 19 5+, 0 6+, 0 7+ spectra with min prob 0.05 Reading in /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_3/interact-CatD_0015_3.pep.xml... ...read in 0 1+, 1350 2+, 1628 3+, 416 4+, 18 5+, 0 6+, 0 7+ spectra with min prob 0.05 Reading in /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_4/interact-CatD_0015_4.pep.xml... ...read in 0 1+, 1551 2+, 1870 3+, 618 4+, 28 5+, 0 6+, 0 7+ spectra with min prob 0.05 Initializing 4839 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Calculating protein lengths and molecular weights from database /home/nanopore-catalyst/centralized_files/proteome_databases/2024-09-16-decoys-contam-mspms_peptide_library.fasta.fas ......WARNING: Found the following zero-mass residues in protein entry TDP163 : IWQKGALHTSLDPQ .WARNING: Found the following zero-mass residues in protein entry TDP167 : HYGFVTKPNHQIWD ..:.........:..WARNING: Found the following zero-mass residues in protein entry TDP90 : NHQLAWGEDRNTFY .......WARNING: Found the following zero-mass residues in protein entry rev_TDP167 : DWIQHNPKTVFGYH :.........:....WARNING: Found the following zero-mass residues in protein entry rev_TDP90 : YFTNRDEGWALQHN .....:.........:......... Total: 692 INFO: mu=0.00304963, db_size=170535 Computing degenerate peptides for 497 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% Computing probabilities for 500 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 500 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 500 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Computing probabilities for 500 proteins. Loop 1: 0%...20%...40%...60%...80%...100% Loop 2: 0%...20%...40%...60%...80%...100% Calculating sensitivity...and error tables... Computing MU for 500 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100% time="18:19:33" level=info msg=Done Process 'ProteinProphet' finished, exit code: 0 PhilosopherDbAnnotate [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher database --annotate /home/nanopore-catalyst/centralized_files/proteome_databases/2024-09-16-decoys-contam-mspms_peptide_library.fasta.fas --prefix rev_ time="18:19:33" level=info msg="Executing Database v5.1.0" time="18:19:33" level=info msg="Annotating the database" time="18:19:33" level=info msg=Done Process 'PhilosopherDbAnnotate' finished, exit code: 0 PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --razor time="18:19:33" level=info msg="Executing Filter v5.1.0" time="18:19:33" level=info msg="Processing peptide identification files" time="18:19:33" level=info msg="Parsing /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1/interact-CatA_0000_1.pep.xml" time="18:19:34" level=info msg="1+ Charge profile" decoy=0 target=0 time="18:19:34" level=info msg="2+ Charge profile" decoy=14 target=1363 time="18:19:34" level=info msg="3+ Charge profile" decoy=39 target=2275 time="18:19:34" level=info msg="4+ Charge profile" decoy=9 target=701 time="18:19:34" level=info msg="5+ Charge profile" decoy=0 target=27 time="18:19:34" level=info msg="6+ Charge profile" decoy=0 target=0 time="18:19:34" level=info msg="Database search results" ions=1197 peptides=811 psms=4428 time="18:19:34" level=info msg="Converged to 0.99 % FDR with 4328 PSMs" decoy=43 threshold=0.668271 total=4371 time="18:19:34" level=info msg="Converged to 0.92 % FDR with 655 Peptides" decoy=6 threshold=0.98928 total=661 time="18:19:34" level=info msg="Converged to 0.94 % FDR with 1069 Ions" decoy=10 threshold=0.958674 total=1079 time="18:19:34" level=info msg="Protein inference results" decoy=159 target=333 time="18:19:34" level=info msg="Converged to 0.86 % FDR with 233 Proteins" decoy=2 threshold=0.999 total=235 time="18:19:34" level=info msg="Applying sequential FDR estimation" ions=1089 peptides=707 psms=4288 time="18:19:34" level=info msg="Converged to 0.02 % FDR with 4287 PSMs" decoy=1 threshold=0.668271 total=4288 time="18:19:34" level=info msg="Converged to 0.14 % FDR with 706 Peptides" decoy=1 threshold=0.671634 total=707 time="18:19:34" level=info msg="Converged to 0.09 % FDR with 1088 Ions" decoy=1 threshold=0.671634 total=1089 time="18:19:34" level=info msg="Post processing identifications" time="18:19:34" level=info msg="Assigning protein identifications to layers" time="18:19:34" level=info msg="Processing protein inference" time="18:19:34" level=info msg="Synchronizing PSMs and proteins" time="18:19:34" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=1088 peptides=706 proteins=209 psms=4287 time="18:19:34" level=info msg=Saving time="18:19:34" level=info msg=Done Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_2 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor time="18:19:34" level=info msg="Executing Filter v5.1.0" time="18:19:34" level=info msg="Fetching protein inference from /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1" time="18:19:34" level=info msg="Processing peptide identification files" time="18:19:34" level=info msg="Parsing /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_2/interact-CatA_0000_2.pep.xml" time="18:19:34" level=info msg="1+ Charge profile" decoy=0 target=0 time="18:19:34" level=info msg="2+ Charge profile" decoy=17 target=1292 time="18:19:34" level=info msg="3+ Charge profile" decoy=30 target=2154 time="18:19:34" level=info msg="4+ Charge profile" decoy=6 target=726 time="18:19:34" level=info msg="5+ Charge profile" decoy=0 target=25 time="18:19:34" level=info msg="6+ Charge profile" decoy=0 target=0 time="18:19:34" level=info msg="Database search results" ions=1155 peptides=787 psms=4250 time="18:19:34" level=info msg="Converged to 0.98 % FDR with 4178 PSMs" decoy=41 threshold=0.62993 total=4219 time="18:19:34" level=info msg="Converged to 0.90 % FDR with 667 Peptides" decoy=6 threshold=0.99225 total=673 time="18:19:34" level=info msg="Converged to 0.98 % FDR with 1022 Ions" decoy=10 threshold=0.985473 total=1032 time="18:19:34" level=info msg="Protein inference results" decoy=159 target=333 time="18:19:34" level=info msg="Converged to 0.86 % FDR with 233 Proteins" decoy=2 threshold=0.999 total=235 time="18:19:34" level=info msg="Applying sequential FDR estimation" ions=1076 peptides=710 psms=4148 time="18:19:34" level=info msg="Converged to 0.02 % FDR with 4147 PSMs" decoy=1 threshold=0.62993 total=4148 time="18:19:34" level=info msg="Converged to 0.14 % FDR with 709 Peptides" decoy=1 threshold=0.710638 total=710 time="18:19:34" level=info msg="Converged to 0.09 % FDR with 1075 Ions" decoy=1 threshold=0.710638 total=1076 time="18:19:34" level=info msg="Post processing identifications" time="18:19:34" level=info msg="Assigning protein identifications to layers" time="18:19:34" level=info msg="Processing protein inference" time="18:19:34" level=info msg="Synchronizing PSMs and proteins" time="18:19:34" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=1075 peptides=709 proteins=207 psms=4147 time="18:19:34" level=info msg=Saving time="18:19:34" level=info msg=Done Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_3 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor time="18:19:34" level=info msg="Executing Filter v5.1.0" time="18:19:34" level=info msg="Fetching protein inference from /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1" time="18:19:34" level=info msg="Processing peptide identification files" time="18:19:34" level=info msg="Parsing /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_3/interact-CatA_0000_3.pep.xml" time="18:19:34" level=info msg="1+ Charge profile" decoy=0 target=0 time="18:19:34" level=info msg="2+ Charge profile" decoy=19 target=1371 time="18:19:34" level=info msg="3+ Charge profile" decoy=41 target=2281 time="18:19:34" level=info msg="4+ Charge profile" decoy=8 target=679 time="18:19:34" level=info msg="5+ Charge profile" decoy=1 target=22 time="18:19:34" level=info msg="6+ Charge profile" decoy=0 target=0 time="18:19:34" level=info msg="Database search results" ions=1198 peptides=823 psms=4422 time="18:19:34" level=info msg="Converged to 0.98 % FDR with 4292 PSMs" decoy=42 threshold=0.702008 total=4334 time="18:19:34" level=info msg="Converged to 0.90 % FDR with 669 Peptides" decoy=6 threshold=0.977621 total=675 time="18:19:34" level=info msg="Converged to 0.96 % FDR with 1043 Ions" decoy=10 threshold=0.962629 total=1053 time="18:19:34" level=info msg="Protein inference results" decoy=159 target=333 time="18:19:34" level=info msg="Converged to 0.86 % FDR with 233 Proteins" decoy=2 threshold=0.999 total=235 time="18:19:35" level=info msg="Applying sequential FDR estimation" ions=1080 peptides=710 psms=4254 time="18:19:35" level=info msg="Converged to 0.00 % FDR with 4254 PSMs" decoy=0 threshold=0.702008 total=4254 time="18:19:35" level=info msg="Converged to 0.00 % FDR with 710 Peptides" decoy=0 threshold=0.723268 total=710 time="18:19:35" level=info msg="Converged to 0.00 % FDR with 1080 Ions" decoy=0 threshold=0.723268 total=1080 time="18:19:35" level=info msg="Post processing identifications" time="18:19:35" level=info msg="Assigning protein identifications to layers" time="18:19:35" level=info msg="Processing protein inference" time="18:19:35" level=info msg="Synchronizing PSMs and proteins" time="18:19:35" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=1080 peptides=710 proteins=212 psms=4254 time="18:19:35" level=info msg=Saving time="18:19:35" level=info msg=Done Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_4 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor time="18:19:35" level=info msg="Executing Filter v5.1.0" time="18:19:35" level=info msg="Fetching protein inference from /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1" time="18:19:35" level=info msg="Processing peptide identification files" time="18:19:35" level=info msg="Parsing /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_4/interact-CatA_0000_4.pep.xml" time="18:19:35" level=info msg="1+ Charge profile" decoy=0 target=0 time="18:19:35" level=info msg="2+ Charge profile" decoy=16 target=1354 time="18:19:35" level=info msg="3+ Charge profile" decoy=30 target=2310 time="18:19:35" level=info msg="4+ Charge profile" decoy=5 target=735 time="18:19:35" level=info msg="5+ Charge profile" decoy=1 target=30 time="18:19:35" level=info msg="6+ Charge profile" decoy=0 target=0 time="18:19:35" level=info msg="Database search results" ions=1183 peptides=798 psms=4481 time="18:19:35" level=info msg="Converged to 1.00 % FDR with 4421 PSMs" decoy=44 threshold=0.561799 total=4465 time="18:19:35" level=info msg="Converged to 0.88 % FDR with 680 Peptides" decoy=6 threshold=0.981374 total=686 time="18:19:35" level=info msg="Converged to 0.93 % FDR with 1070 Ions" decoy=10 threshold=0.954488 total=1080 time="18:19:35" level=info msg="Protein inference results" decoy=159 target=333 time="18:19:35" level=info msg="Converged to 0.86 % FDR with 233 Proteins" decoy=2 threshold=0.999 total=235 time="18:19:35" level=info msg="Applying sequential FDR estimation" ions=1103 peptides=722 psms=4379 time="18:19:35" level=info msg="Converged to 0.00 % FDR with 4379 PSMs" decoy=0 threshold=0.561799 total=4379 time="18:19:35" level=info msg="Converged to 0.00 % FDR with 722 Peptides" decoy=0 threshold=0.610752 total=722 time="18:19:35" level=info msg="Converged to 0.00 % FDR with 1103 Ions" decoy=0 threshold=0.610752 total=1103 time="18:19:35" level=info msg="Post processing identifications" time="18:19:35" level=info msg="Assigning protein identifications to layers" time="18:19:35" level=info msg="Processing protein inference" time="18:19:35" level=info msg="Synchronizing PSMs and proteins" time="18:19:35" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=1103 peptides=722 proteins=210 psms=4379 time="18:19:35" level=info msg=Saving time="18:19:35" level=info msg=Done Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_1 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor time="18:19:35" level=info msg="Executing Filter v5.1.0" time="18:19:35" level=info msg="Fetching protein inference from /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1" time="18:19:35" level=info msg="Processing peptide identification files" time="18:19:35" level=info msg="Parsing /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_1/interact-CatA_0030_1.pep.xml" time="18:19:35" level=info msg="1+ Charge profile" decoy=0 target=0 time="18:19:35" level=info msg="2+ Charge profile" decoy=16 target=1347 time="18:19:35" level=info msg="3+ Charge profile" decoy=42 target=2144 time="18:19:35" level=info msg="4+ Charge profile" decoy=7 target=675 time="18:19:35" level=info msg="5+ Charge profile" decoy=0 target=23 time="18:19:35" level=info msg="6+ Charge profile" decoy=0 target=0 time="18:19:35" level=info msg="Database search results" ions=1416 peptides=979 psms=4254 time="18:19:35" level=info msg="Converged to 0.99 % FDR with 4162 PSMs" decoy=41 threshold=0.65683 total=4203 time="18:19:35" level=info msg="Converged to 0.92 % FDR with 872 Peptides" decoy=8 threshold=0.962105 total=880 time="18:19:35" level=info msg="Converged to 0.99 % FDR with 1313 Ions" decoy=13 threshold=0.90881 total=1326 time="18:19:35" level=info msg="Protein inference results" decoy=159 target=333 time="18:19:35" level=info msg="Converged to 0.86 % FDR with 233 Proteins" decoy=2 threshold=0.999 total=235 time="18:19:35" level=info msg="Applying sequential FDR estimation" ions=1319 peptides=885 psms=4127 time="18:19:35" level=info msg="Converged to 0.00 % FDR with 4127 PSMs" decoy=0 threshold=0.657031 total=4127 time="18:19:35" level=info msg="Converged to 0.00 % FDR with 885 Peptides" decoy=0 threshold=0.659523 total=885 time="18:19:35" level=info msg="Converged to 0.00 % FDR with 1319 Ions" decoy=0 threshold=0.659523 total=1319 time="18:19:35" level=info msg="Post processing identifications" time="18:19:35" level=info msg="Assigning protein identifications to layers" time="18:19:35" level=info msg="Processing protein inference" time="18:19:35" level=info msg="Synchronizing PSMs and proteins" time="18:19:35" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=1319 peptides=885 proteins=219 psms=4127 time="18:19:35" level=info msg=Saving time="18:19:35" level=info msg=Done Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_2 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor time="18:19:36" level=info msg="Executing Filter v5.1.0" time="18:19:36" level=info msg="Fetching protein inference from /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1" time="18:19:36" level=info msg="Processing peptide identification files" time="18:19:36" level=info msg="Parsing /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_2/interact-CatA_0030_2.pep.xml" time="18:19:36" level=info msg="1+ Charge profile" decoy=0 target=0 time="18:19:36" level=info msg="2+ Charge profile" decoy=15 target=1286 time="18:19:36" level=info msg="3+ Charge profile" decoy=40 target=2062 time="18:19:36" level=info msg="4+ Charge profile" decoy=5 target=677 time="18:19:36" level=info msg="5+ Charge profile" decoy=0 target=19 time="18:19:36" level=info msg="6+ Charge profile" decoy=0 target=0 time="18:19:36" level=info msg="Database search results" ions=1349 peptides=931 psms=4104 time="18:19:36" level=info msg="Converged to 0.98 % FDR with 3988 PSMs" decoy=39 threshold=0.708578 total=4027 time="18:19:36" level=info msg="Converged to 0.94 % FDR with 850 Peptides" decoy=8 threshold=0.932603 total=858 time="18:19:36" level=info msg="Converged to 0.95 % FDR with 1264 Ions" decoy=12 threshold=0.901094 total=1276 time="18:19:36" level=info msg="Protein inference results" decoy=159 target=333 time="18:19:36" level=info msg="Converged to 0.86 % FDR with 233 Proteins" decoy=2 threshold=0.999 total=235 time="18:19:36" level=info msg="Applying sequential FDR estimation" ions=1272 peptides=858 psms=3971 time="18:19:36" level=info msg="Converged to 0.00 % FDR with 3971 PSMs" decoy=0 threshold=0.716352 total=3971 time="18:19:36" level=info msg="Converged to 0.00 % FDR with 858 Peptides" decoy=0 threshold=0.719663 total=858 time="18:19:36" level=info msg="Converged to 0.00 % FDR with 1272 Ions" decoy=0 threshold=0.719663 total=1272 time="18:19:36" level=info msg="Post processing identifications" time="18:19:36" level=info msg="Assigning protein identifications to layers" time="18:19:36" level=info msg="Processing protein inference" time="18:19:36" level=info msg="Synchronizing PSMs and proteins" time="18:19:36" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=1272 peptides=858 proteins=217 psms=3971 time="18:19:36" level=info msg=Saving time="18:19:36" level=info msg=Done Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_3 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor time="18:19:36" level=info msg="Executing Filter v5.1.0" time="18:19:36" level=info msg="Fetching protein inference from /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1" time="18:19:36" level=info msg="Processing peptide identification files" time="18:19:36" level=info msg="Parsing /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_3/interact-CatA_0030_3.pep.xml" time="18:19:36" level=info msg="1+ Charge profile" decoy=0 target=0 time="18:19:36" level=info msg="2+ Charge profile" decoy=15 target=1319 time="18:19:36" level=info msg="3+ Charge profile" decoy=25 target=2161 time="18:19:36" level=info msg="4+ Charge profile" decoy=6 target=745 time="18:19:36" level=info msg="5+ Charge profile" decoy=0 target=25 time="18:19:36" level=info msg="6+ Charge profile" decoy=0 target=0 time="18:19:36" level=info msg="Database search results" ions=1363 peptides=930 psms=4296 time="18:19:36" level=info msg="Converged to 0.99 % FDR with 4242 PSMs" decoy=42 threshold=0.55959 total=4284 time="18:19:36" level=info msg="Converged to 0.95 % FDR with 846 Peptides" decoy=8 threshold=0.957395 total=854 time="18:19:36" level=info msg="Converged to 0.93 % FDR with 1295 Ions" decoy=12 threshold=0.839134 total=1307 time="18:19:36" level=info msg="Protein inference results" decoy=159 target=333 time="18:19:36" level=info msg="Converged to 0.86 % FDR with 233 Proteins" decoy=2 threshold=0.999 total=235 time="18:19:36" level=info msg="Applying sequential FDR estimation" ions=1286 peptides=857 psms=4203 time="18:19:36" level=info msg="Converged to 0.02 % FDR with 4202 PSMs" decoy=1 threshold=0.574473 total=4203 time="18:19:36" level=info msg="Converged to 0.12 % FDR with 856 Peptides" decoy=1 threshold=0.574473 total=857 time="18:19:36" level=info msg="Converged to 0.08 % FDR with 1285 Ions" decoy=1 threshold=0.574473 total=1286 time="18:19:36" level=info msg="Post processing identifications" time="18:19:36" level=info msg="Assigning protein identifications to layers" time="18:19:36" level=info msg="Processing protein inference" time="18:19:36" level=info msg="Synchronizing PSMs and proteins" time="18:19:36" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=1285 peptides=856 proteins=217 psms=4202 time="18:19:36" level=info msg=Saving time="18:19:36" level=info msg=Done Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_4 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor time="18:19:36" level=info msg="Executing Filter v5.1.0" time="18:19:36" level=info msg="Fetching protein inference from /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1" time="18:19:36" level=info msg="Processing peptide identification files" time="18:19:36" level=info msg="Parsing /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_4/interact-CatA_0030_4.pep.xml" time="18:19:37" level=info msg="1+ Charge profile" decoy=0 target=0 time="18:19:37" level=info msg="2+ Charge profile" decoy=20 target=1518 time="18:19:37" level=info msg="3+ Charge profile" decoy=44 target=2336 time="18:19:37" level=info msg="4+ Charge profile" decoy=12 target=790 time="18:19:37" level=info msg="5+ Charge profile" decoy=1 target=25 time="18:19:37" level=info msg="6+ Charge profile" decoy=0 target=0 time="18:19:37" level=info msg="Database search results" ions=1460 peptides=1014 psms=4746 time="18:19:37" level=info msg="Converged to 1.00 % FDR with 4615 PSMs" decoy=46 threshold=0.718082 total=4661 time="18:19:37" level=info msg="Converged to 0.94 % FDR with 854 Peptides" decoy=8 threshold=0.979284 total=862 time="18:19:37" level=info msg="Converged to 1.00 % FDR with 1303 Ions" decoy=13 threshold=0.959418 total=1316 time="18:19:37" level=info msg="Protein inference results" decoy=159 target=333 time="18:19:37" level=info msg="Converged to 0.86 % FDR with 233 Proteins" decoy=2 threshold=0.999 total=235 time="18:19:37" level=info msg="Applying sequential FDR estimation" ions=1346 peptides=903 psms=4582 time="18:19:37" level=info msg="Converged to 0.04 % FDR with 4580 PSMs" decoy=2 threshold=0.726891 total=4582 time="18:19:37" level=info msg="Converged to 0.22 % FDR with 901 Peptides" decoy=2 threshold=0.726891 total=903 time="18:19:37" level=info msg="Converged to 0.15 % FDR with 1344 Ions" decoy=2 threshold=0.726891 total=1346 time="18:19:37" level=info msg="Post processing identifications" time="18:19:37" level=info msg="Assigning protein identifications to layers" time="18:19:37" level=info msg="Processing protein inference" time="18:19:37" level=info msg="Synchronizing PSMs and proteins" time="18:19:37" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=1344 peptides=901 proteins=216 psms=4580 time="18:19:37" level=info msg=Saving time="18:19:37" level=info msg=Done Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_1 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor time="18:19:37" level=info msg="Executing Filter v5.1.0" time="18:19:37" level=info msg="Fetching protein inference from /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1" time="18:19:37" level=info msg="Processing peptide identification files" time="18:19:37" level=info msg="Parsing /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_1/interact-CatA_0090_1.pep.xml" time="18:19:37" level=info msg="1+ Charge profile" decoy=0 target=0 time="18:19:37" level=info msg="2+ Charge profile" decoy=15 target=1390 time="18:19:37" level=info msg="3+ Charge profile" decoy=31 target=2118 time="18:19:37" level=info msg="4+ Charge profile" decoy=6 target=742 time="18:19:37" level=info msg="5+ Charge profile" decoy=1 target=18 time="18:19:37" level=info msg="6+ Charge profile" decoy=0 target=0 time="18:19:37" level=info msg="Database search results" ions=1409 peptides=962 psms=4321 time="18:19:37" level=info msg="Converged to 0.99 % FDR with 4249 PSMs" decoy=42 threshold=0.618584 total=4291 time="18:19:37" level=info msg="Converged to 0.95 % FDR with 845 Peptides" decoy=8 threshold=0.984064 total=853 time="18:19:37" level=info msg="Converged to 0.93 % FDR with 1294 Ions" decoy=12 threshold=0.965259 total=1306 time="18:19:37" level=info msg="Protein inference results" decoy=159 target=333 time="18:19:37" level=info msg="Converged to 0.86 % FDR with 233 Proteins" decoy=2 threshold=0.999 total=235 time="18:19:37" level=info msg="Applying sequential FDR estimation" ions=1322 peptides=879 psms=4209 time="18:19:37" level=info msg="Converged to 0.05 % FDR with 4207 PSMs" decoy=2 threshold=0.636769 total=4209 time="18:19:37" level=info msg="Converged to 0.23 % FDR with 877 Peptides" decoy=2 threshold=0.695991 total=879 time="18:19:37" level=info msg="Converged to 0.15 % FDR with 1320 Ions" decoy=2 threshold=0.653698 total=1322 time="18:19:37" level=info msg="Post processing identifications" time="18:19:37" level=info msg="Assigning protein identifications to layers" time="18:19:37" level=info msg="Processing protein inference" time="18:19:37" level=info msg="Synchronizing PSMs and proteins" time="18:19:37" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=1320 peptides=877 proteins=216 psms=4207 time="18:19:37" level=info msg=Saving time="18:19:37" level=info msg=Done Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_2 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor time="18:19:37" level=info msg="Executing Filter v5.1.0" time="18:19:37" level=info msg="Fetching protein inference from /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1" time="18:19:37" level=info msg="Processing peptide identification files" time="18:19:37" level=info msg="Parsing /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_2/interact-CatA_0090_2.pep.xml" time="18:19:37" level=info msg="1+ Charge profile" decoy=0 target=0 time="18:19:37" level=info msg="2+ Charge profile" decoy=17 target=1358 time="18:19:37" level=info msg="3+ Charge profile" decoy=23 target=2097 time="18:19:37" level=info msg="4+ Charge profile" decoy=7 target=711 time="18:19:37" level=info msg="5+ Charge profile" decoy=0 target=15 time="18:19:37" level=info msg="6+ Charge profile" decoy=0 target=0 time="18:19:37" level=info msg="Database search results" ions=1384 peptides=940 psms=4228 time="18:19:37" level=info msg="Converged to 0.98 % FDR with 4178 PSMs" decoy=41 threshold=0.553396 total=4219 time="18:19:37" level=info msg="Converged to 0.95 % FDR with 838 Peptides" decoy=8 threshold=0.973404 total=846 time="18:19:37" level=info msg="Converged to 1.00 % FDR with 1302 Ions" decoy=13 threshold=0.917156 total=1315 time="18:19:37" level=info msg="Protein inference results" decoy=159 target=333 time="18:19:37" level=info msg="Converged to 0.86 % FDR with 233 Proteins" decoy=2 threshold=0.999 total=235 time="18:19:37" level=info msg="Applying sequential FDR estimation" ions=1319 peptides=876 psms=4150 time="18:19:37" level=info msg="Converged to 0.05 % FDR with 4148 PSMs" decoy=2 threshold=0.553396 total=4150 time="18:19:37" level=info msg="Converged to 0.23 % FDR with 874 Peptides" decoy=2 threshold=0.553396 total=876 time="18:19:37" level=info msg="Converged to 0.15 % FDR with 1317 Ions" decoy=2 threshold=0.553396 total=1319 time="18:19:37" level=info msg="Post processing identifications" time="18:19:37" level=info msg="Assigning protein identifications to layers" time="18:19:37" level=info msg="Processing protein inference" time="18:19:37" level=info msg="Synchronizing PSMs and proteins" time="18:19:37" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=1317 peptides=874 proteins=214 psms=4148 time="18:19:37" level=info msg=Saving time="18:19:37" level=info msg=Done Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_3 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor time="18:19:38" level=info msg="Executing Filter v5.1.0" time="18:19:38" level=info msg="Fetching protein inference from /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1" time="18:19:38" level=info msg="Processing peptide identification files" time="18:19:38" level=info msg="Parsing /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_3/interact-CatA_0090_3.pep.xml" time="18:19:38" level=info msg="1+ Charge profile" decoy=0 target=0 time="18:19:38" level=info msg="2+ Charge profile" decoy=17 target=1444 time="18:19:38" level=info msg="3+ Charge profile" decoy=40 target=2064 time="18:19:38" level=info msg="4+ Charge profile" decoy=5 target=692 time="18:19:38" level=info msg="5+ Charge profile" decoy=0 target=20 time="18:19:38" level=info msg="6+ Charge profile" decoy=0 target=0 time="18:19:38" level=info msg="Database search results" ions=1388 peptides=949 psms=4282 time="18:19:38" level=info msg="Converged to 0.99 % FDR with 4158 PSMs" decoy=41 threshold=0.743091 total=4199 time="18:19:38" level=info msg="Converged to 0.97 % FDR with 829 Peptides" decoy=8 threshold=0.980681 total=837 time="18:19:38" level=info msg="Converged to 0.94 % FDR with 1273 Ions" decoy=12 threshold=0.955265 total=1285 time="18:19:38" level=info msg="Protein inference results" decoy=159 target=333 time="18:19:38" level=info msg="Converged to 0.86 % FDR with 233 Proteins" decoy=2 threshold=0.999 total=235 time="18:19:38" level=info msg="Applying sequential FDR estimation" ions=1294 peptides=862 psms=4136 time="18:19:38" level=info msg="Converged to 0.02 % FDR with 4135 PSMs" decoy=1 threshold=0.749885 total=4136 time="18:19:38" level=info msg="Converged to 0.12 % FDR with 861 Peptides" decoy=1 threshold=0.753635 total=862 time="18:19:38" level=info msg="Converged to 0.08 % FDR with 1293 Ions" decoy=1 threshold=0.753635 total=1294 time="18:19:38" level=info msg="Post processing identifications" time="18:19:38" level=info msg="Assigning protein identifications to layers" time="18:19:38" level=info msg="Processing protein inference" time="18:19:38" level=info msg="Synchronizing PSMs and proteins" time="18:19:38" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=1293 peptides=861 proteins=217 psms=4135 time="18:19:38" level=info msg=Saving time="18:19:38" level=info msg=Done Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_4 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor time="18:19:38" level=info msg="Executing Filter v5.1.0" time="18:19:38" level=info msg="Fetching protein inference from /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1" time="18:19:38" level=info msg="Processing peptide identification files" time="18:19:38" level=info msg="Parsing /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_4/interact-CatA_0090_4.pep.xml" time="18:19:38" level=info msg="1+ Charge profile" decoy=0 target=0 time="18:19:38" level=info msg="2+ Charge profile" decoy=13 target=1394 time="18:19:38" level=info msg="3+ Charge profile" decoy=37 target=2078 time="18:19:38" level=info msg="4+ Charge profile" decoy=9 target=679 time="18:19:38" level=info msg="5+ Charge profile" decoy=0 target=21 time="18:19:38" level=info msg="6+ Charge profile" decoy=0 target=0 time="18:19:38" level=info msg="Database search results" ions=1383 peptides=949 psms=4231 time="18:19:38" level=info msg="Converged to 0.99 % FDR with 4146 PSMs" decoy=41 threshold=0.632861 total=4187 time="18:19:38" level=info msg="Converged to 1.00 % FDR with 802 Peptides" decoy=8 threshold=0.989617 total=810 time="18:19:38" level=info msg="Converged to 0.95 % FDR with 1257 Ions" decoy=12 threshold=0.965022 total=1269 time="18:19:38" level=info msg="Protein inference results" decoy=159 target=333 time="18:19:38" level=info msg="Converged to 0.86 % FDR with 233 Proteins" decoy=2 threshold=0.999 total=235 time="18:19:38" level=info msg="Applying sequential FDR estimation" ions=1302 peptides=869 psms=4127 time="18:19:38" level=info msg="Converged to 0.05 % FDR with 4125 PSMs" decoy=2 threshold=0.642449 total=4127 time="18:19:38" level=info msg="Converged to 0.23 % FDR with 867 Peptides" decoy=2 threshold=0.726064 total=869 time="18:19:38" level=info msg="Converged to 0.15 % FDR with 1300 Ions" decoy=2 threshold=0.642449 total=1302 time="18:19:38" level=info msg="Post processing identifications" time="18:19:38" level=info msg="Assigning protein identifications to layers" time="18:19:38" level=info msg="Processing protein inference" time="18:19:38" level=info msg="Synchronizing PSMs and proteins" time="18:19:38" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=1300 peptides=867 proteins=219 psms=4125 time="18:19:38" level=info msg=Saving time="18:19:38" level=info msg=Done Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_1 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor time="18:19:38" level=info msg="Executing Filter v5.1.0" time="18:19:38" level=info msg="Fetching protein inference from /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1" time="18:19:38" level=info msg="Processing peptide identification files" time="18:19:38" level=info msg="Parsing /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_1/interact-CatB_0000_1.pep.xml" time="18:19:39" level=info msg="1+ Charge profile" decoy=0 target=0 time="18:19:39" level=info msg="2+ Charge profile" decoy=25 target=1408 time="18:19:39" level=info msg="3+ Charge profile" decoy=45 target=1828 time="18:19:39" level=info msg="4+ Charge profile" decoy=7 target=399 time="18:19:39" level=info msg="5+ Charge profile" decoy=2 target=15 time="18:19:39" level=info msg="6+ Charge profile" decoy=0 target=0 time="18:19:39" level=info msg="Database search results" ions=1403 peptides=972 psms=3729 time="18:19:39" level=info msg="Converged to 0.99 % FDR with 3552 PSMs" decoy=35 threshold=0.714638 total=3587 time="18:19:39" level=info msg="Converged to 0.97 % FDR with 828 Peptides" decoy=8 threshold=0.901426 total=836 time="18:19:39" level=info msg="Converged to 0.96 % FDR with 1252 Ions" decoy=12 threshold=0.860968 total=1264 time="18:19:39" level=info msg="Protein inference results" decoy=159 target=333 time="18:19:39" level=info msg="Converged to 0.86 % FDR with 233 Proteins" decoy=2 threshold=0.999 total=235 time="18:19:39" level=info msg="Applying sequential FDR estimation" ions=1252 peptides=830 psms=3517 time="18:19:39" level=info msg="Converged to 0.00 % FDR with 3517 PSMs" decoy=0 threshold=0.716867 total=3517 time="18:19:39" level=info msg="Converged to 0.00 % FDR with 830 Peptides" decoy=0 threshold=0.742988 total=830 time="18:19:39" level=info msg="Converged to 0.00 % FDR with 1252 Ions" decoy=0 threshold=0.742988 total=1252 time="18:19:39" level=info msg="Post processing identifications" time="18:19:39" level=info msg="Assigning protein identifications to layers" time="18:19:39" level=info msg="Processing protein inference" time="18:19:39" level=info msg="Synchronizing PSMs and proteins" time="18:19:39" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=1252 peptides=830 proteins=224 psms=3517 time="18:19:39" level=info msg=Saving time="18:19:39" level=info msg=Done Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_2 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor time="18:19:39" level=info msg="Executing Filter v5.1.0" time="18:19:39" level=info msg="Fetching protein inference from /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1" time="18:19:39" level=info msg="Processing peptide identification files" time="18:19:39" level=info msg="Parsing /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_2/interact-CatB_0000_2.pep.xml" time="18:19:39" level=info msg="1+ Charge profile" decoy=0 target=0 time="18:19:39" level=info msg="2+ Charge profile" decoy=21 target=1458 time="18:19:39" level=info msg="3+ Charge profile" decoy=40 target=1978 time="18:19:39" level=info msg="4+ Charge profile" decoy=9 target=396 time="18:19:39" level=info msg="5+ Charge profile" decoy=0 target=10 time="18:19:39" level=info msg="6+ Charge profile" decoy=0 target=0 time="18:19:39" level=info msg="Database search results" ions=1338 peptides=922 psms=3912 time="18:19:39" level=info msg="Converged to 0.98 % FDR with 3764 PSMs" decoy=37 threshold=0.695208 total=3801 time="18:19:39" level=info msg="Converged to 0.88 % FDR with 795 Peptides" decoy=7 threshold=0.949332 total=802 time="18:19:39" level=info msg="Converged to 0.92 % FDR with 1198 Ions" decoy=11 threshold=0.935414 total=1209 time="18:19:39" level=info msg="Protein inference results" decoy=159 target=333 time="18:19:39" level=info msg="Converged to 0.86 % FDR with 233 Proteins" decoy=2 threshold=0.999 total=235 time="18:19:39" level=info msg="Applying sequential FDR estimation" ions=1219 peptides=811 psms=3737 time="18:19:39" level=info msg="Converged to 0.00 % FDR with 3737 PSMs" decoy=0 threshold=0.695208 total=3737 time="18:19:39" level=info msg="Converged to 0.00 % FDR with 811 Peptides" decoy=0 threshold=0.695784 total=811 time="18:19:39" level=info msg="Converged to 0.00 % FDR with 1219 Ions" decoy=0 threshold=0.695784 total=1219 time="18:19:39" level=info msg="Post processing identifications" time="18:19:39" level=info msg="Assigning protein identifications to layers" time="18:19:39" level=info msg="Processing protein inference" time="18:19:39" level=info msg="Synchronizing PSMs and proteins" time="18:19:39" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=1219 peptides=811 proteins=223 psms=3737 time="18:19:39" level=info msg=Saving time="18:19:39" level=info msg=Done Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_3 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor time="18:19:39" level=info msg="Executing Filter v5.1.0" time="18:19:39" level=info msg="Fetching protein inference from /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1" time="18:19:39" level=info msg="Processing peptide identification files" time="18:19:39" level=info msg="Parsing /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_3/interact-CatB_0000_3.pep.xml" time="18:19:39" level=info msg="1+ Charge profile" decoy=0 target=0 time="18:19:39" level=info msg="2+ Charge profile" decoy=33 target=1700 time="18:19:39" level=info msg="3+ Charge profile" decoy=47 target=2076 time="18:19:39" level=info msg="4+ Charge profile" decoy=14 target=478 time="18:19:39" level=info msg="5+ Charge profile" decoy=1 target=16 time="18:19:39" level=info msg="6+ Charge profile" decoy=0 target=0 time="18:19:39" level=info msg="Database search results" ions=1470 peptides=1003 psms=4365 time="18:19:39" level=info msg="Converged to 0.98 % FDR with 4094 PSMs" decoy=40 threshold=0.796631 total=4134 time="18:19:39" level=info msg="Converged to 0.98 % FDR with 816 Peptides" decoy=8 threshold=0.970053 total=824 time="18:19:39" level=info msg="Converged to 0.95 % FDR with 1269 Ions" decoy=12 threshold=0.933291 total=1281 time="18:19:39" level=info msg="Protein inference results" decoy=159 target=333 time="18:19:39" level=info msg="Converged to 0.86 % FDR with 233 Proteins" decoy=2 threshold=0.999 total=235 time="18:19:39" level=info msg="Applying sequential FDR estimation" ions=1300 peptides=849 psms=4073 time="18:19:39" level=info msg="Converged to 0.00 % FDR with 4073 PSMs" decoy=0 threshold=0.796631 total=4073 time="18:19:39" level=info msg="Converged to 0.00 % FDR with 849 Peptides" decoy=0 threshold=0.810156 total=849 time="18:19:39" level=info msg="Converged to 0.00 % FDR with 1300 Ions" decoy=0 threshold=0.810156 total=1300 time="18:19:39" level=info msg="Post processing identifications" time="18:19:39" level=info msg="Assigning protein identifications to layers" time="18:19:39" level=info msg="Processing protein inference" time="18:19:39" level=info msg="Synchronizing PSMs and proteins" time="18:19:39" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=1300 peptides=849 proteins=224 psms=4073 time="18:19:39" level=info msg=Saving time="18:19:40" level=info msg=Done Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_4 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor time="18:19:40" level=info msg="Executing Filter v5.1.0" time="18:19:40" level=info msg="Fetching protein inference from /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1" time="18:19:40" level=info msg="Processing peptide identification files" time="18:19:40" level=info msg="Parsing /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_4/interact-CatB_0000_4.pep.xml" time="18:19:40" level=info msg="1+ Charge profile" decoy=0 target=0 time="18:19:40" level=info msg="2+ Charge profile" decoy=26 target=1760 time="18:19:40" level=info msg="3+ Charge profile" decoy=36 target=2084 time="18:19:40" level=info msg="4+ Charge profile" decoy=9 target=456 time="18:19:40" level=info msg="5+ Charge profile" decoy=3 target=18 time="18:19:40" level=info msg="6+ Charge profile" decoy=0 target=0 time="18:19:40" level=info msg="Database search results" ions=1427 peptides=970 psms=4392 time="18:19:40" level=info msg="Converged to 1.00 % FDR with 4216 PSMs" decoy=42 threshold=0.759058 total=4258 time="18:19:40" level=info msg="Converged to 0.95 % FDR with 839 Peptides" decoy=8 threshold=0.936767 total=847 time="18:19:40" level=info msg="Converged to 0.94 % FDR with 1280 Ions" decoy=12 threshold=0.917368 total=1292 time="18:19:40" level=info msg="Protein inference results" decoy=159 target=333 time="18:19:40" level=info msg="Converged to 0.86 % FDR with 233 Proteins" decoy=2 threshold=0.999 total=235 time="18:19:40" level=info msg="Applying sequential FDR estimation" ions=1293 peptides=845 psms=4180 time="18:19:40" level=info msg="Converged to 0.00 % FDR with 4180 PSMs" decoy=0 threshold=0.759058 total=4180 time="18:19:40" level=info msg="Converged to 0.00 % FDR with 845 Peptides" decoy=0 threshold=0.760969 total=845 time="18:19:40" level=info msg="Converged to 0.00 % FDR with 1293 Ions" decoy=0 threshold=0.760969 total=1293 time="18:19:40" level=info msg="Post processing identifications" time="18:19:40" level=info msg="Assigning protein identifications to layers" time="18:19:40" level=info msg="Processing protein inference" time="18:19:40" level=info msg="Synchronizing PSMs and proteins" time="18:19:40" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=1293 peptides=845 proteins=226 psms=4180 time="18:19:40" level=info msg=Saving time="18:19:40" level=info msg=Done Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_1 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor time="18:19:40" level=info msg="Executing Filter v5.1.0" time="18:19:40" level=info msg="Fetching protein inference from /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1" time="18:19:40" level=info msg="Processing peptide identification files" time="18:19:40" level=info msg="Parsing /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_1/interact-CatB_0015_1.pep.xml" time="18:19:40" level=info msg="1+ Charge profile" decoy=0 target=0 time="18:19:40" level=info msg="2+ Charge profile" decoy=22 target=1613 time="18:19:40" level=info msg="3+ Charge profile" decoy=46 target=2020 time="18:19:40" level=info msg="4+ Charge profile" decoy=17 target=503 time="18:19:40" level=info msg="5+ Charge profile" decoy=4 target=17 time="18:19:40" level=info msg="6+ Charge profile" decoy=0 target=0 time="18:19:40" level=info msg="Database search results" ions=1612 peptides=1111 psms=4242 time="18:19:40" level=info msg="Converged to 0.98 % FDR with 3990 PSMs" decoy=39 threshold=0.792452 total=4029 time="18:19:40" level=info msg="Converged to 0.97 % FDR with 927 Peptides" decoy=9 threshold=0.946328 total=936 time="18:19:40" level=info msg="Converged to 0.98 % FDR with 1429 Ions" decoy=14 threshold=0.902407 total=1443 time="18:19:40" level=info msg="Protein inference results" decoy=159 target=333 time="18:19:40" level=info msg="Converged to 0.86 % FDR with 233 Proteins" decoy=2 threshold=0.999 total=235 time="18:19:40" level=info msg="Applying sequential FDR estimation" ions=1432 peptides=942 psms=3954 time="18:19:40" level=info msg="Converged to 0.00 % FDR with 3954 PSMs" decoy=0 threshold=0.797041 total=3954 time="18:19:40" level=info msg="Converged to 0.00 % FDR with 942 Peptides" decoy=0 threshold=0.797041 total=942 time="18:19:40" level=info msg="Converged to 0.00 % FDR with 1432 Ions" decoy=0 threshold=0.797041 total=1432 time="18:19:40" level=info msg="Post processing identifications" time="18:19:40" level=info msg="Assigning protein identifications to layers" time="18:19:40" level=info msg="Processing protein inference" time="18:19:40" level=info msg="Synchronizing PSMs and proteins" time="18:19:40" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=1432 peptides=942 proteins=226 psms=3954 time="18:19:40" level=info msg=Saving time="18:19:40" level=info msg=Done Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_2 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor time="18:19:40" level=info msg="Executing Filter v5.1.0" time="18:19:40" level=info msg="Fetching protein inference from /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1" time="18:19:41" level=info msg="Processing peptide identification files" time="18:19:41" level=info msg="Parsing /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_2/interact-CatB_0015_2.pep.xml" time="18:19:41" level=info msg="1+ Charge profile" decoy=0 target=0 time="18:19:41" level=info msg="2+ Charge profile" decoy=21 target=1719 time="18:19:41" level=info msg="3+ Charge profile" decoy=44 target=1995 time="18:19:41" level=info msg="4+ Charge profile" decoy=7 target=362 time="18:19:41" level=info msg="5+ Charge profile" decoy=1 target=11 time="18:19:41" level=info msg="6+ Charge profile" decoy=0 target=0 time="18:19:41" level=info msg="Database search results" ions=1512 peptides=1058 psms=4160 time="18:19:41" level=info msg="Converged to 0.98 % FDR with 3994 PSMs" decoy=39 threshold=0.745712 total=4033 time="18:19:41" level=info msg="Converged to 0.99 % FDR with 907 Peptides" decoy=9 threshold=0.946586 total=916 time="18:19:41" level=info msg="Converged to 0.96 % FDR with 1353 Ions" decoy=13 threshold=0.932404 total=1366 time="18:19:41" level=info msg="Protein inference results" decoy=159 target=333 time="18:19:41" level=info msg="Converged to 0.86 % FDR with 233 Proteins" decoy=2 threshold=0.999 total=235 time="18:19:41" level=info msg="Applying sequential FDR estimation" ions=1371 peptides=921 psms=3960 time="18:19:41" level=info msg="Converged to 0.00 % FDR with 3960 PSMs" decoy=0 threshold=0.748761 total=3960 time="18:19:41" level=info msg="Converged to 0.00 % FDR with 921 Peptides" decoy=0 threshold=0.756178 total=921 time="18:19:41" level=info msg="Converged to 0.00 % FDR with 1371 Ions" decoy=0 threshold=0.756178 total=1371 time="18:19:41" level=info msg="Post processing identifications" time="18:19:41" level=info msg="Assigning protein identifications to layers" time="18:19:41" level=info msg="Processing protein inference" time="18:19:41" level=info msg="Synchronizing PSMs and proteins" time="18:19:41" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=1371 peptides=921 proteins=222 psms=3960 time="18:19:41" level=info msg=Saving time="18:19:41" level=info msg=Done Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_3 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor time="18:19:41" level=info msg="Executing Filter v5.1.0" time="18:19:41" level=info msg="Fetching protein inference from /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1" time="18:19:41" level=info msg="Processing peptide identification files" time="18:19:41" level=info msg="Parsing /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_3/interact-CatB_0015_3.pep.xml" time="18:19:41" level=info msg="1+ Charge profile" decoy=0 target=0 time="18:19:41" level=info msg="2+ Charge profile" decoy=22 target=1710 time="18:19:41" level=info msg="3+ Charge profile" decoy=51 target=2156 time="18:19:41" level=info msg="4+ Charge profile" decoy=11 target=518 time="18:19:41" level=info msg="5+ Charge profile" decoy=2 target=16 time="18:19:41" level=info msg="6+ Charge profile" decoy=0 target=0 time="18:19:41" level=info msg="Database search results" ions=1581 peptides=1084 psms=4486 time="18:19:41" level=info msg="Converged to 0.98 % FDR with 4282 PSMs" decoy=42 threshold=0.746955 total=4324 time="18:19:41" level=info msg="Converged to 0.97 % FDR with 926 Peptides" decoy=9 threshold=0.935262 total=935 time="18:19:41" level=info msg="Converged to 0.99 % FDR with 1414 Ions" decoy=14 threshold=0.904948 total=1428 time="18:19:41" level=info msg="Protein inference results" decoy=159 target=333 time="18:19:41" level=info msg="Converged to 0.86 % FDR with 233 Proteins" decoy=2 threshold=0.999 total=235 time="18:19:41" level=info msg="Applying sequential FDR estimation" ions=1426 peptides=937 psms=4249 time="18:19:41" level=info msg="Converged to 0.00 % FDR with 4249 PSMs" decoy=0 threshold=0.748832 total=4249 time="18:19:41" level=info msg="Converged to 0.00 % FDR with 937 Peptides" decoy=0 threshold=0.754435 total=937 time="18:19:41" level=info msg="Converged to 0.00 % FDR with 1426 Ions" decoy=0 threshold=0.753458 total=1426 time="18:19:41" level=info msg="Post processing identifications" time="18:19:41" level=info msg="Assigning protein identifications to layers" time="18:19:41" level=info msg="Processing protein inference" time="18:19:41" level=info msg="Synchronizing PSMs and proteins" time="18:19:41" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=1426 peptides=937 proteins=223 psms=4249 time="18:19:41" level=info msg=Saving time="18:19:41" level=info msg=Done Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_4 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor time="18:19:41" level=info msg="Executing Filter v5.1.0" time="18:19:41" level=info msg="Fetching protein inference from /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1" time="18:19:41" level=info msg="Processing peptide identification files" time="18:19:41" level=info msg="Parsing /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_4/interact-CatB_0015_4.pep.xml" time="18:19:41" level=info msg="1+ Charge profile" decoy=0 target=0 time="18:19:41" level=info msg="2+ Charge profile" decoy=34 target=1726 time="18:19:41" level=info msg="3+ Charge profile" decoy=58 target=2184 time="18:19:41" level=info msg="4+ Charge profile" decoy=15 target=519 time="18:19:41" level=info msg="5+ Charge profile" decoy=2 target=19 time="18:19:41" level=info msg="6+ Charge profile" decoy=0 target=0 time="18:19:41" level=info msg="Database search results" ions=1638 peptides=1134 psms=4557 time="18:19:41" level=info msg="Converged to 0.99 % FDR with 4255 PSMs" decoy=42 threshold=0.789798 total=4297 time="18:19:41" level=info msg="Converged to 0.97 % FDR with 932 Peptides" decoy=9 threshold=0.952352 total=941 time="18:19:42" level=info msg="Converged to 0.98 % FDR with 1427 Ions" decoy=14 threshold=0.926244 total=1441 time="18:19:42" level=info msg="Protein inference results" decoy=159 target=333 time="18:19:42" level=info msg="Converged to 0.86 % FDR with 233 Proteins" decoy=2 threshold=0.999 total=235 time="18:19:42" level=info msg="Applying sequential FDR estimation" ions=1448 peptides=954 psms=4222 time="18:19:42" level=info msg="Converged to 0.00 % FDR with 4222 PSMs" decoy=0 threshold=0.792368 total=4222 time="18:19:42" level=info msg="Converged to 0.00 % FDR with 954 Peptides" decoy=0 threshold=0.792368 total=954 time="18:19:42" level=info msg="Converged to 0.00 % FDR with 1448 Ions" decoy=0 threshold=0.792368 total=1448 time="18:19:42" level=info msg="Post processing identifications" time="18:19:42" level=info msg="Assigning protein identifications to layers" time="18:19:42" level=info msg="Processing protein inference" time="18:19:42" level=info msg="Synchronizing PSMs and proteins" time="18:19:42" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=1448 peptides=954 proteins=224 psms=4222 time="18:19:42" level=info msg=Saving time="18:19:42" level=info msg=Done Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_1 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor time="18:19:42" level=info msg="Executing Filter v5.1.0" time="18:19:42" level=info msg="Fetching protein inference from /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1" time="18:19:42" level=info msg="Processing peptide identification files" time="18:19:42" level=info msg="Parsing /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_1/interact-CatB_0060_1.pep.xml" time="18:19:42" level=info msg="1+ Charge profile" decoy=0 target=0 time="18:19:42" level=info msg="2+ Charge profile" decoy=22 target=1605 time="18:19:42" level=info msg="3+ Charge profile" decoy=42 target=2102 time="18:19:42" level=info msg="4+ Charge profile" decoy=11 target=491 time="18:19:42" level=info msg="5+ Charge profile" decoy=1 target=17 time="18:19:42" level=info msg="6+ Charge profile" decoy=0 target=0 time="18:19:42" level=info msg="Database search results" ions=1651 peptides=1133 psms=4291 time="18:19:42" level=info msg="Converged to 0.98 % FDR with 4092 PSMs" decoy=40 threshold=0.773841 total=4132 time="18:19:42" level=info msg="Converged to 0.93 % FDR with 972 Peptides" decoy=9 threshold=0.948311 total=981 time="18:19:42" level=info msg="Converged to 1.00 % FDR with 1500 Ions" decoy=15 threshold=0.903212 total=1515 time="18:19:42" level=info msg="Protein inference results" decoy=159 target=333 time="18:19:42" level=info msg="Converged to 0.86 % FDR with 233 Proteins" decoy=2 threshold=0.999 total=235 time="18:19:42" level=info msg="Applying sequential FDR estimation" ions=1505 peptides=994 psms=4052 time="18:19:42" level=info msg="Converged to 0.00 % FDR with 4052 PSMs" decoy=0 threshold=0.773841 total=4052 time="18:19:42" level=info msg="Converged to 0.00 % FDR with 994 Peptides" decoy=0 threshold=0.782703 total=994 time="18:19:42" level=info msg="Converged to 0.00 % FDR with 1505 Ions" decoy=0 threshold=0.782703 total=1505 time="18:19:42" level=info msg="Post processing identifications" time="18:19:42" level=info msg="Assigning protein identifications to layers" time="18:19:42" level=info msg="Processing protein inference" time="18:19:42" level=info msg="Synchronizing PSMs and proteins" time="18:19:42" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=1505 peptides=994 proteins=226 psms=4052 time="18:19:42" level=info msg=Saving time="18:19:42" level=info msg=Done Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_2 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor time="18:19:42" level=info msg="Executing Filter v5.1.0" time="18:19:42" level=info msg="Fetching protein inference from /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1" time="18:19:42" level=info msg="Processing peptide identification files" time="18:19:42" level=info msg="Parsing /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_2/interact-CatB_0060_2.pep.xml" time="18:19:42" level=info msg="1+ Charge profile" decoy=0 target=0 time="18:19:42" level=info msg="2+ Charge profile" decoy=24 target=1611 time="18:19:42" level=info msg="3+ Charge profile" decoy=44 target=2099 time="18:19:42" level=info msg="4+ Charge profile" decoy=10 target=528 time="18:19:42" level=info msg="5+ Charge profile" decoy=1 target=17 time="18:19:42" level=info msg="6+ Charge profile" decoy=0 target=0 time="18:19:42" level=info msg="Database search results" ions=1647 peptides=1122 psms=4334 time="18:19:42" level=info msg="Converged to 1.00 % FDR with 4105 PSMs" decoy=41 threshold=0.792265 total=4146 time="18:19:42" level=info msg="Converged to 0.93 % FDR with 964 Peptides" decoy=9 threshold=0.958525 total=973 time="18:19:42" level=info msg="Converged to 0.95 % FDR with 1473 Ions" decoy=14 threshold=0.929305 total=1487 time="18:19:42" level=info msg="Protein inference results" decoy=159 target=333 time="18:19:42" level=info msg="Converged to 0.86 % FDR with 233 Proteins" decoy=2 threshold=0.999 total=235 time="18:19:42" level=info msg="Applying sequential FDR estimation" ions=1501 peptides=987 psms=4080 time="18:19:42" level=info msg="Converged to 0.00 % FDR with 4080 PSMs" decoy=0 threshold=0.792769 total=4080 time="18:19:42" level=info msg="Converged to 0.00 % FDR with 987 Peptides" decoy=0 threshold=0.792769 total=987 time="18:19:42" level=info msg="Converged to 0.00 % FDR with 1501 Ions" decoy=0 threshold=0.792769 total=1501 time="18:19:42" level=info msg="Post processing identifications" time="18:19:42" level=info msg="Assigning protein identifications to layers" time="18:19:42" level=info msg="Processing protein inference" time="18:19:42" level=info msg="Synchronizing PSMs and proteins" time="18:19:42" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=1501 peptides=987 proteins=224 psms=4080 time="18:19:42" level=info msg=Saving time="18:19:42" level=info msg=Done Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_3 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor time="18:19:43" level=info msg="Executing Filter v5.1.0" time="18:19:43" level=info msg="Fetching protein inference from /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1" time="18:19:43" level=info msg="Processing peptide identification files" time="18:19:43" level=info msg="Parsing /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_3/interact-CatB_0060_3.pep.xml" time="18:19:43" level=info msg="1+ Charge profile" decoy=0 target=0 time="18:19:43" level=info msg="2+ Charge profile" decoy=28 target=1722 time="18:19:43" level=info msg="3+ Charge profile" decoy=61 target=2174 time="18:19:43" level=info msg="4+ Charge profile" decoy=10 target=510 time="18:19:43" level=info msg="5+ Charge profile" decoy=2 target=18 time="18:19:43" level=info msg="6+ Charge profile" decoy=0 target=0 time="18:19:43" level=info msg="Database search results" ions=1805 peptides=1273 psms=4525 time="18:19:43" level=info msg="Converged to 0.98 % FDR with 4284 PSMs" decoy=42 threshold=0.764461 total=4326 time="18:19:43" level=info msg="Converged to 0.95 % FDR with 1056 Peptides" decoy=10 threshold=0.947771 total=1066 time="18:19:43" level=info msg="Converged to 0.95 % FDR with 1582 Ions" decoy=15 threshold=0.908218 total=1597 time="18:19:43" level=info msg="Protein inference results" decoy=159 target=333 time="18:19:43" level=info msg="Converged to 0.86 % FDR with 233 Proteins" decoy=2 threshold=0.999 total=235 time="18:19:43" level=info msg="Applying sequential FDR estimation" ions=1604 peptides=1081 psms=4252 time="18:19:43" level=info msg="Converged to 0.00 % FDR with 4252 PSMs" decoy=0 threshold=0.769553 total=4252 time="18:19:43" level=info msg="Converged to 0.00 % FDR with 1081 Peptides" decoy=0 threshold=0.773029 total=1081 time="18:19:43" level=info msg="Converged to 0.00 % FDR with 1604 Ions" decoy=0 threshold=0.773029 total=1604 time="18:19:43" level=info msg="Post processing identifications" time="18:19:43" level=info msg="Assigning protein identifications to layers" time="18:19:43" level=info msg="Processing protein inference" time="18:19:43" level=info msg="Synchronizing PSMs and proteins" time="18:19:43" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=1604 peptides=1081 proteins=228 psms=4252 time="18:19:43" level=info msg=Saving time="18:19:43" level=info msg=Done Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_4 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor time="18:19:43" level=info msg="Executing Filter v5.1.0" time="18:19:43" level=info msg="Fetching protein inference from /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1" time="18:19:43" level=info msg="Processing peptide identification files" time="18:19:43" level=info msg="Parsing /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_4/interact-CatB_0060_4.pep.xml" time="18:19:43" level=info msg="1+ Charge profile" decoy=0 target=0 time="18:19:43" level=info msg="2+ Charge profile" decoy=25 target=1682 time="18:19:43" level=info msg="3+ Charge profile" decoy=52 target=2140 time="18:19:43" level=info msg="4+ Charge profile" decoy=13 target=490 time="18:19:43" level=info msg="5+ Charge profile" decoy=0 target=13 time="18:19:43" level=info msg="6+ Charge profile" decoy=0 target=0 time="18:19:43" level=info msg="Database search results" ions=1688 peptides=1152 psms=4415 time="18:19:43" level=info msg="Converged to 0.98 % FDR with 4178 PSMs" decoy=41 threshold=0.75392 total=4219 time="18:19:43" level=info msg="Converged to 0.91 % FDR with 985 Peptides" decoy=9 threshold=0.938134 total=994 time="18:19:43" level=info msg="Converged to 0.98 % FDR with 1528 Ions" decoy=15 threshold=0.866676 total=1543 time="18:19:43" level=info msg="Protein inference results" decoy=159 target=333 time="18:19:43" level=info msg="Converged to 0.86 % FDR with 233 Proteins" decoy=2 threshold=0.999 total=235 time="18:19:43" level=info msg="Applying sequential FDR estimation" ions=1520 peptides=996 psms=4148 time="18:19:43" level=info msg="Converged to 0.00 % FDR with 4148 PSMs" decoy=0 threshold=0.756578 total=4148 time="18:19:43" level=info msg="Converged to 0.00 % FDR with 996 Peptides" decoy=0 threshold=0.765885 total=996 time="18:19:43" level=info msg="Converged to 0.00 % FDR with 1520 Ions" decoy=0 threshold=0.765885 total=1520 time="18:19:43" level=info msg="Post processing identifications" time="18:19:43" level=info msg="Assigning protein identifications to layers" time="18:19:43" level=info msg="Processing protein inference" time="18:19:43" level=info msg="Synchronizing PSMs and proteins" time="18:19:43" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=1520 peptides=996 proteins=224 psms=4148 time="18:19:43" level=info msg=Saving time="18:19:43" level=info msg=Done Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_1 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor time="18:19:43" level=info msg="Executing Filter v5.1.0" time="18:19:43" level=info msg="Fetching protein inference from /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1" time="18:19:43" level=info msg="Processing peptide identification files" time="18:19:43" level=info msg="Parsing /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_1/interact-CatC_0000_1.pep.xml" time="18:19:44" level=info msg="1+ Charge profile" decoy=0 target=0 time="18:19:44" level=info msg="2+ Charge profile" decoy=28 target=1836 time="18:19:44" level=info msg="3+ Charge profile" decoy=42 target=2751 time="18:19:44" level=info msg="4+ Charge profile" decoy=11 target=755 time="18:19:44" level=info msg="5+ Charge profile" decoy=1 target=32 time="18:19:44" level=info msg="6+ Charge profile" decoy=0 target=0 time="18:19:44" level=info msg="Database search results" ions=1318 peptides=888 psms=5456 time="18:19:44" level=info msg="Converged to 1.00 % FDR with 5307 PSMs" decoy=53 threshold=0.683334 total=5360 time="18:19:44" level=info msg="Converged to 0.92 % FDR with 759 Peptides" decoy=7 threshold=0.954238 total=766 time="18:19:44" level=info msg="Converged to 0.93 % FDR with 1180 Ions" decoy=11 threshold=0.93925 total=1191 time="18:19:44" level=info msg="Protein inference results" decoy=159 target=333 time="18:19:44" level=info msg="Converged to 0.86 % FDR with 233 Proteins" decoy=2 threshold=0.999 total=235 time="18:19:44" level=info msg="Applying sequential FDR estimation" ions=1197 peptides=771 psms=5280 time="18:19:44" level=info msg="Converged to 0.04 % FDR with 5278 PSMs" decoy=2 threshold=0.690814 total=5280 time="18:19:44" level=info msg="Converged to 0.26 % FDR with 769 Peptides" decoy=2 threshold=0.699678 total=771 time="18:19:44" level=info msg="Converged to 0.17 % FDR with 1195 Ions" decoy=2 threshold=0.699678 total=1197 time="18:19:44" level=info msg="Post processing identifications" time="18:19:44" level=info msg="Assigning protein identifications to layers" time="18:19:44" level=info msg="Processing protein inference" time="18:19:44" level=info msg="Synchronizing PSMs and proteins" time="18:19:44" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=1195 peptides=769 proteins=215 psms=5278 time="18:19:44" level=info msg=Saving time="18:19:44" level=info msg=Done Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_2 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor time="18:19:44" level=info msg="Executing Filter v5.1.0" time="18:19:44" level=info msg="Fetching protein inference from /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1" time="18:19:44" level=info msg="Processing peptide identification files" time="18:19:44" level=info msg="Parsing /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_2/interact-CatC_0000_2.pep.xml" time="18:19:44" level=info msg="1+ Charge profile" decoy=0 target=0 time="18:19:44" level=info msg="2+ Charge profile" decoy=24 target=1865 time="18:19:44" level=info msg="3+ Charge profile" decoy=50 target=2839 time="18:19:44" level=info msg="4+ Charge profile" decoy=11 target=856 time="18:19:44" level=info msg="5+ Charge profile" decoy=0 target=30 time="18:19:44" level=info msg="6+ Charge profile" decoy=0 target=0 time="18:19:44" level=info msg="Database search results" ions=1320 peptides=899 psms=5675 time="18:19:44" level=info msg="Converged to 0.99 % FDR with 5535 PSMs" decoy=55 threshold=0.655411 total=5590 time="18:19:44" level=info msg="Converged to 0.95 % FDR with 735 Peptides" decoy=7 threshold=0.977166 total=742 time="18:19:44" level=info msg="Converged to 0.95 % FDR with 1164 Ions" decoy=11 threshold=0.940811 total=1175 time="18:19:44" level=info msg="Protein inference results" decoy=159 target=333 time="18:19:44" level=info msg="Converged to 0.86 % FDR with 233 Proteins" decoy=2 threshold=0.999 total=235 time="18:19:44" level=info msg="Applying sequential FDR estimation" ions=1180 peptides=766 psms=5492 time="18:19:44" level=info msg="Converged to 0.02 % FDR with 5491 PSMs" decoy=1 threshold=0.656435 total=5492 time="18:19:44" level=info msg="Converged to 0.13 % FDR with 765 Peptides" decoy=1 threshold=0.667057 total=766 time="18:19:44" level=info msg="Converged to 0.08 % FDR with 1179 Ions" decoy=1 threshold=0.656435 total=1180 time="18:19:44" level=info msg="Post processing identifications" time="18:19:44" level=info msg="Assigning protein identifications to layers" time="18:19:44" level=info msg="Processing protein inference" time="18:19:44" level=info msg="Synchronizing PSMs and proteins" time="18:19:44" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=1179 peptides=765 proteins=215 psms=5491 time="18:19:44" level=info msg=Saving time="18:19:44" level=info msg=Done Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_3 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor time="18:19:44" level=info msg="Executing Filter v5.1.0" time="18:19:44" level=info msg="Fetching protein inference from /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1" time="18:19:44" level=info msg="Processing peptide identification files" time="18:19:44" level=info msg="Parsing /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_3/interact-CatC_0000_3.pep.xml" time="18:19:44" level=info msg="1+ Charge profile" decoy=0 target=0 time="18:19:44" level=info msg="2+ Charge profile" decoy=25 target=1815 time="18:19:44" level=info msg="3+ Charge profile" decoy=35 target=2761 time="18:19:44" level=info msg="4+ Charge profile" decoy=9 target=802 time="18:19:44" level=info msg="5+ Charge profile" decoy=0 target=34 time="18:19:44" level=info msg="6+ Charge profile" decoy=0 target=0 time="18:19:44" level=info msg="Database search results" ions=1279 peptides=875 psms=5481 time="18:19:44" level=info msg="Converged to 0.98 % FDR with 5385 PSMs" decoy=53 threshold=0.607238 total=5438 time="18:19:44" level=info msg="Converged to 0.93 % FDR with 749 Peptides" decoy=7 threshold=0.958488 total=756 time="18:19:44" level=info msg="Converged to 0.96 % FDR with 1145 Ions" decoy=11 threshold=0.952017 total=1156 time="18:19:44" level=info msg="Protein inference results" decoy=159 target=333 time="18:19:44" level=info msg="Converged to 0.86 % FDR with 233 Proteins" decoy=2 threshold=0.999 total=235 time="18:19:44" level=info msg="Applying sequential FDR estimation" ions=1173 peptides=772 psms=5339 time="18:19:44" level=info msg="Converged to 0.02 % FDR with 5338 PSMs" decoy=1 threshold=0.609462 total=5339 time="18:19:44" level=info msg="Converged to 0.13 % FDR with 771 Peptides" decoy=1 threshold=0.621298 total=772 time="18:19:44" level=info msg="Converged to 0.09 % FDR with 1172 Ions" decoy=1 threshold=0.621298 total=1173 time="18:19:44" level=info msg="Post processing identifications" time="18:19:44" level=info msg="Assigning protein identifications to layers" time="18:19:44" level=info msg="Processing protein inference" time="18:19:44" level=info msg="Synchronizing PSMs and proteins" time="18:19:44" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=1172 peptides=771 proteins=218 psms=5338 time="18:19:44" level=info msg=Saving time="18:19:44" level=info msg=Done Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_4 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor time="18:19:45" level=info msg="Executing Filter v5.1.0" time="18:19:45" level=info msg="Fetching protein inference from /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1" time="18:19:45" level=info msg="Processing peptide identification files" time="18:19:45" level=info msg="Parsing /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_4/interact-CatC_0000_4.pep.xml" time="18:19:45" level=info msg="1+ Charge profile" decoy=0 target=0 time="18:19:45" level=info msg="2+ Charge profile" decoy=20 target=1847 time="18:19:45" level=info msg="3+ Charge profile" decoy=43 target=2785 time="18:19:45" level=info msg="4+ Charge profile" decoy=17 target=870 time="18:19:45" level=info msg="5+ Charge profile" decoy=0 target=32 time="18:19:45" level=info msg="6+ Charge profile" decoy=0 target=0 time="18:19:45" level=info msg="Database search results" ions=1345 peptides=918 psms=5614 time="18:19:45" level=info msg="Converged to 0.98 % FDR with 5485 PSMs" decoy=54 threshold=0.629968 total=5539 time="18:19:45" level=info msg="Converged to 0.92 % FDR with 765 Peptides" decoy=7 threshold=0.969369 total=772 time="18:19:45" level=info msg="Converged to 0.93 % FDR with 1189 Ions" decoy=11 threshold=0.938379 total=1200 time="18:19:45" level=info msg="Protein inference results" decoy=159 target=333 time="18:19:45" level=info msg="Converged to 0.86 % FDR with 233 Proteins" decoy=2 threshold=0.999 total=235 time="18:19:45" level=info msg="Applying sequential FDR estimation" ions=1200 peptides=779 psms=5435 time="18:19:45" level=info msg="Converged to 0.02 % FDR with 5434 PSMs" decoy=1 threshold=0.633409 total=5435 time="18:19:45" level=info msg="Converged to 0.13 % FDR with 778 Peptides" decoy=1 threshold=0.674399 total=779 time="18:19:45" level=info msg="Converged to 0.08 % FDR with 1199 Ions" decoy=1 threshold=0.674399 total=1200 time="18:19:45" level=info msg="Post processing identifications" time="18:19:45" level=info msg="Assigning protein identifications to layers" time="18:19:45" level=info msg="Processing protein inference" time="18:19:45" level=info msg="Synchronizing PSMs and proteins" time="18:19:45" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=1199 peptides=778 proteins=216 psms=5434 time="18:19:45" level=info msg=Saving time="18:19:45" level=info msg=Done Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_1 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor time="18:19:45" level=info msg="Executing Filter v5.1.0" time="18:19:45" level=info msg="Fetching protein inference from /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1" time="18:19:45" level=info msg="Processing peptide identification files" time="18:19:45" level=info msg="Parsing /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_1/interact-CatC_0030_1.pep.xml" time="18:19:45" level=info msg="1+ Charge profile" decoy=0 target=0 time="18:19:45" level=info msg="2+ Charge profile" decoy=24 target=1835 time="18:19:45" level=info msg="3+ Charge profile" decoy=42 target=2707 time="18:19:45" level=info msg="4+ Charge profile" decoy=8 target=764 time="18:19:45" level=info msg="5+ Charge profile" decoy=0 target=29 time="18:19:45" level=info msg="6+ Charge profile" decoy=0 target=0 time="18:19:45" level=info msg="Database search results" ions=1371 peptides=925 psms=5409 time="18:19:45" level=info msg="Converged to 0.98 % FDR with 5288 PSMs" decoy=52 threshold=0.648934 total=5340 time="18:19:45" level=info msg="Converged to 0.91 % FDR with 768 Peptides" decoy=7 threshold=0.98841 total=775 time="18:19:45" level=info msg="Converged to 0.97 % FDR with 1233 Ions" decoy=12 threshold=0.955746 total=1245 time="18:19:45" level=info msg="Protein inference results" decoy=159 target=333 time="18:19:45" level=info msg="Converged to 0.86 % FDR with 233 Proteins" decoy=2 threshold=0.999 total=235 time="18:19:45" level=info msg="Applying sequential FDR estimation" ions=1248 peptides=805 psms=5242 time="18:19:45" level=info msg="Converged to 0.02 % FDR with 5241 PSMs" decoy=1 threshold=0.649259 total=5242 time="18:19:45" level=info msg="Converged to 0.12 % FDR with 804 Peptides" decoy=1 threshold=0.661574 total=805 time="18:19:45" level=info msg="Converged to 0.08 % FDR with 1247 Ions" decoy=1 threshold=0.661574 total=1248 time="18:19:45" level=info msg="Post processing identifications" time="18:19:45" level=info msg="Assigning protein identifications to layers" time="18:19:45" level=info msg="Processing protein inference" time="18:19:45" level=info msg="Synchronizing PSMs and proteins" time="18:19:45" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=1247 peptides=804 proteins=218 psms=5241 time="18:19:45" level=info msg=Saving time="18:19:45" level=info msg=Done Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_2 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor time="18:19:45" level=info msg="Executing Filter v5.1.0" time="18:19:45" level=info msg="Fetching protein inference from /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1" time="18:19:45" level=info msg="Processing peptide identification files" time="18:19:45" level=info msg="Parsing /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_2/interact-CatC_0030_2.pep.xml" time="18:19:46" level=info msg="1+ Charge profile" decoy=0 target=0 time="18:19:46" level=info msg="2+ Charge profile" decoy=22 target=1818 time="18:19:46" level=info msg="3+ Charge profile" decoy=49 target=2722 time="18:19:46" level=info msg="4+ Charge profile" decoy=11 target=810 time="18:19:46" level=info msg="5+ Charge profile" decoy=2 target=29 time="18:19:46" level=info msg="6+ Charge profile" decoy=0 target=0 time="18:19:46" level=info msg="Database search results" ions=1391 peptides=925 psms=5463 time="18:19:46" level=info msg="Converged to 1.00 % FDR with 5313 PSMs" decoy=53 threshold=0.679127 total=5366 time="18:19:46" level=info msg="Converged to 0.91 % FDR with 771 Peptides" decoy=7 threshold=0.96917 total=778 time="18:19:46" level=info msg="Converged to 0.97 % FDR with 1231 Ions" decoy=12 threshold=0.94863 total=1243 time="18:19:46" level=info msg="Protein inference results" decoy=159 target=333 time="18:19:46" level=info msg="Converged to 0.86 % FDR with 233 Proteins" decoy=2 threshold=0.999 total=235 time="18:19:46" level=info msg="Applying sequential FDR estimation" ions=1250 peptides=791 psms=5273 time="18:19:46" level=info msg="Converged to 0.02 % FDR with 5272 PSMs" decoy=1 threshold=0.683333 total=5273 time="18:19:46" level=info msg="Converged to 0.13 % FDR with 790 Peptides" decoy=1 threshold=0.705968 total=791 time="18:19:46" level=info msg="Converged to 0.08 % FDR with 1249 Ions" decoy=1 threshold=0.705968 total=1250 time="18:19:46" level=info msg="Post processing identifications" time="18:19:46" level=info msg="Assigning protein identifications to layers" time="18:19:46" level=info msg="Processing protein inference" time="18:19:46" level=info msg="Synchronizing PSMs and proteins" time="18:19:46" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=1249 peptides=790 proteins=216 psms=5272 time="18:19:46" level=info msg=Saving time="18:19:46" level=info msg=Done Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_3 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor time="18:19:46" level=info msg="Executing Filter v5.1.0" time="18:19:46" level=info msg="Fetching protein inference from /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1" time="18:19:46" level=info msg="Processing peptide identification files" time="18:19:46" level=info msg="Parsing /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_3/interact-CatC_0030_3.pep.xml" time="18:19:46" level=info msg="1+ Charge profile" decoy=0 target=0 time="18:19:46" level=info msg="2+ Charge profile" decoy=18 target=1918 time="18:19:46" level=info msg="3+ Charge profile" decoy=55 target=2823 time="18:19:46" level=info msg="4+ Charge profile" decoy=9 target=809 time="18:19:46" level=info msg="5+ Charge profile" decoy=0 target=32 time="18:19:46" level=info msg="6+ Charge profile" decoy=0 target=0 time="18:19:46" level=info msg="Database search results" ions=1399 peptides=949 psms=5664 time="18:19:46" level=info msg="Converged to 1.00 % FDR with 5517 PSMs" decoy=55 threshold=0.675718 total=5572 time="18:19:46" level=info msg="Converged to 0.99 % FDR with 808 Peptides" decoy=8 threshold=0.945875 total=816 time="18:19:46" level=info msg="Converged to 0.95 % FDR with 1261 Ions" decoy=12 threshold=0.901591 total=1273 time="18:19:46" level=info msg="Protein inference results" decoy=159 target=333 time="18:19:46" level=info msg="Converged to 0.86 % FDR with 233 Proteins" decoy=2 threshold=0.999 total=235 time="18:19:46" level=info msg="Applying sequential FDR estimation" ions=1261 peptides=815 psms=5472 time="18:19:46" level=info msg="Converged to 0.02 % FDR with 5471 PSMs" decoy=1 threshold=0.675718 total=5472 time="18:19:46" level=info msg="Converged to 0.12 % FDR with 814 Peptides" decoy=1 threshold=0.714098 total=815 time="18:19:46" level=info msg="Converged to 0.08 % FDR with 1260 Ions" decoy=1 threshold=0.714098 total=1261 time="18:19:46" level=info msg="Post processing identifications" time="18:19:46" level=info msg="Assigning protein identifications to layers" time="18:19:46" level=info msg="Processing protein inference" time="18:19:46" level=info msg="Synchronizing PSMs and proteins" time="18:19:46" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=1260 peptides=814 proteins=217 psms=5471 time="18:19:46" level=info msg=Saving time="18:19:46" level=info msg=Done Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_4 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor time="18:19:46" level=info msg="Executing Filter v5.1.0" time="18:19:46" level=info msg="Fetching protein inference from /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1" time="18:19:46" level=info msg="Processing peptide identification files" time="18:19:46" level=info msg="Parsing /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_4/interact-CatC_0030_4.pep.xml" time="18:19:46" level=info msg="1+ Charge profile" decoy=0 target=0 time="18:19:46" level=info msg="2+ Charge profile" decoy=18 target=1801 time="18:19:46" level=info msg="3+ Charge profile" decoy=42 target=2745 time="18:19:46" level=info msg="4+ Charge profile" decoy=10 target=822 time="18:19:46" level=info msg="5+ Charge profile" decoy=2 target=34 time="18:19:46" level=info msg="6+ Charge profile" decoy=0 target=0 time="18:19:46" level=info msg="Database search results" ions=1366 peptides=919 psms=5474 time="18:19:46" level=info msg="Converged to 0.99 % FDR with 5359 PSMs" decoy=53 threshold=0.637472 total=5412 time="18:19:46" level=info msg="Converged to 0.91 % FDR with 772 Peptides" decoy=7 threshold=0.981901 total=779 time="18:19:46" level=info msg="Converged to 0.96 % FDR with 1244 Ions" decoy=12 threshold=0.905522 total=1256 time="18:19:46" level=info msg="Protein inference results" decoy=159 target=333 time="18:19:46" level=info msg="Converged to 0.86 % FDR with 233 Proteins" decoy=2 threshold=0.999 total=235 time="18:19:46" level=info msg="Applying sequential FDR estimation" ions=1247 peptides=805 psms=5316 time="18:19:46" level=info msg="Converged to 0.04 % FDR with 5314 PSMs" decoy=2 threshold=0.637982 total=5316 time="18:19:46" level=info msg="Converged to 0.25 % FDR with 803 Peptides" decoy=2 threshold=0.655124 total=805 time="18:19:46" level=info msg="Converged to 0.16 % FDR with 1245 Ions" decoy=2 threshold=0.655124 total=1247 time="18:19:46" level=info msg="Post processing identifications" time="18:19:46" level=info msg="Assigning protein identifications to layers" time="18:19:46" level=info msg="Processing protein inference" time="18:19:46" level=info msg="Synchronizing PSMs and proteins" time="18:19:46" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=1245 peptides=803 proteins=214 psms=5314 time="18:19:46" level=info msg=Saving time="18:19:46" level=info msg=Done Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_1 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor time="18:19:47" level=info msg="Executing Filter v5.1.0" time="18:19:47" level=info msg="Fetching protein inference from /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1" time="18:19:47" level=info msg="Processing peptide identification files" time="18:19:47" level=info msg="Parsing /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_1/interact-CatC_0090_1.pep.xml" time="18:19:47" level=info msg="1+ Charge profile" decoy=0 target=0 time="18:19:47" level=info msg="2+ Charge profile" decoy=25 target=1809 time="18:19:47" level=info msg="3+ Charge profile" decoy=43 target=2633 time="18:19:47" level=info msg="4+ Charge profile" decoy=12 target=795 time="18:19:47" level=info msg="5+ Charge profile" decoy=2 target=28 time="18:19:47" level=info msg="6+ Charge profile" decoy=0 target=0 time="18:19:47" level=info msg="Database search results" ions=1423 peptides=959 psms=5347 time="18:19:47" level=info msg="Converged to 0.98 % FDR with 5184 PSMs" decoy=51 threshold=0.695202 total=5235 time="18:19:47" level=info msg="Converged to 0.98 % FDR with 814 Peptides" decoy=8 threshold=0.968824 total=822 time="18:19:47" level=info msg="Converged to 0.95 % FDR with 1262 Ions" decoy=12 threshold=0.963011 total=1274 time="18:19:47" level=info msg="Protein inference results" decoy=159 target=333 time="18:19:47" level=info msg="Converged to 0.86 % FDR with 233 Proteins" decoy=2 threshold=0.999 total=235 time="18:19:47" level=info msg="Applying sequential FDR estimation" ions=1302 peptides=846 psms=5156 time="18:19:47" level=info msg="Converged to 0.02 % FDR with 5155 PSMs" decoy=1 threshold=0.695202 total=5156 time="18:19:47" level=info msg="Converged to 0.12 % FDR with 845 Peptides" decoy=1 threshold=0.695202 total=846 time="18:19:47" level=info msg="Converged to 0.08 % FDR with 1301 Ions" decoy=1 threshold=0.695202 total=1302 time="18:19:47" level=info msg="Post processing identifications" time="18:19:47" level=info msg="Assigning protein identifications to layers" time="18:19:47" level=info msg="Processing protein inference" time="18:19:47" level=info msg="Synchronizing PSMs and proteins" time="18:19:47" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=1301 peptides=845 proteins=218 psms=5155 time="18:19:47" level=info msg=Saving time="18:19:47" level=info msg=Done Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_2 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor time="18:19:47" level=info msg="Executing Filter v5.1.0" time="18:19:47" level=info msg="Fetching protein inference from /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1" time="18:19:47" level=info msg="Processing peptide identification files" time="18:19:47" level=info msg="Parsing /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_2/interact-CatC_0090_2.pep.xml" time="18:19:47" level=info msg="1+ Charge profile" decoy=0 target=0 time="18:19:47" level=info msg="2+ Charge profile" decoy=27 target=1951 time="18:19:47" level=info msg="3+ Charge profile" decoy=56 target=2733 time="18:19:47" level=info msg="4+ Charge profile" decoy=14 target=793 time="18:19:47" level=info msg="5+ Charge profile" decoy=2 target=31 time="18:19:47" level=info msg="6+ Charge profile" decoy=0 target=0 time="18:19:47" level=info msg="Database search results" ions=1480 peptides=1006 psms=5607 time="18:19:47" level=info msg="Converged to 1.00 % FDR with 5420 PSMs" decoy=54 threshold=0.717867 total=5474 time="18:19:47" level=info msg="Converged to 0.95 % FDR with 842 Peptides" decoy=8 threshold=0.949859 total=850 time="18:19:47" level=info msg="Converged to 0.99 % FDR with 1311 Ions" decoy=13 threshold=0.927731 total=1324 time="18:19:47" level=info msg="Protein inference results" decoy=159 target=333 time="18:19:47" level=info msg="Converged to 0.86 % FDR with 233 Proteins" decoy=2 threshold=0.999 total=235 time="18:19:47" level=info msg="Applying sequential FDR estimation" ions=1326 peptides=857 psms=5385 time="18:19:47" level=info msg="Converged to 0.02 % FDR with 5384 PSMs" decoy=1 threshold=0.717867 total=5385 time="18:19:47" level=info msg="Converged to 0.12 % FDR with 856 Peptides" decoy=1 threshold=0.740502 total=857 time="18:19:47" level=info msg="Converged to 0.08 % FDR with 1325 Ions" decoy=1 threshold=0.740502 total=1326 time="18:19:47" level=info msg="Post processing identifications" time="18:19:47" level=info msg="Assigning protein identifications to layers" time="18:19:47" level=info msg="Processing protein inference" time="18:19:47" level=info msg="Synchronizing PSMs and proteins" time="18:19:47" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=1325 peptides=856 proteins=223 psms=5384 time="18:19:47" level=info msg=Saving time="18:19:47" level=info msg=Done Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_3 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor time="18:19:47" level=info msg="Executing Filter v5.1.0" time="18:19:47" level=info msg="Fetching protein inference from /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1" time="18:19:47" level=info msg="Processing peptide identification files" time="18:19:47" level=info msg="Parsing /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_3/interact-CatC_0090_3.pep.xml" time="18:19:48" level=info msg="1+ Charge profile" decoy=0 target=0 time="18:19:48" level=info msg="2+ Charge profile" decoy=23 target=1912 time="18:19:48" level=info msg="3+ Charge profile" decoy=48 target=2731 time="18:19:48" level=info msg="4+ Charge profile" decoy=12 target=804 time="18:19:48" level=info msg="5+ Charge profile" decoy=1 target=31 time="18:19:48" level=info msg="6+ Charge profile" decoy=0 target=0 time="18:19:48" level=info msg="Database search results" ions=1457 peptides=987 psms=5562 time="18:19:48" level=info msg="Converged to 1.00 % FDR with 5405 PSMs" decoy=54 threshold=0.712659 total=5459 time="18:19:48" level=info msg="Converged to 0.98 % FDR with 820 Peptides" decoy=8 threshold=0.981479 total=828 time="18:19:48" level=info msg="Converged to 1.00 % FDR with 1305 Ions" decoy=13 threshold=0.949304 total=1318 time="18:19:48" level=info msg="Protein inference results" decoy=159 target=333 time="18:19:48" level=info msg="Converged to 0.86 % FDR with 233 Proteins" decoy=2 threshold=0.999 total=235 time="18:19:48" level=info msg="Applying sequential FDR estimation" ions=1319 peptides=853 psms=5357 time="18:19:48" level=info msg="Converged to 0.00 % FDR with 5357 PSMs" decoy=0 threshold=0.712659 total=5357 time="18:19:48" level=info msg="Converged to 0.00 % FDR with 853 Peptides" decoy=0 threshold=0.716217 total=853 time="18:19:48" level=info msg="Converged to 0.00 % FDR with 1319 Ions" decoy=0 threshold=0.716217 total=1319 time="18:19:48" level=info msg="Post processing identifications" time="18:19:48" level=info msg="Assigning protein identifications to layers" time="18:19:48" level=info msg="Processing protein inference" time="18:19:48" level=info msg="Synchronizing PSMs and proteins" time="18:19:48" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=1319 peptides=853 proteins=218 psms=5357 time="18:19:48" level=info msg=Saving time="18:19:48" level=info msg=Done Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_4 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor time="18:19:48" level=info msg="Executing Filter v5.1.0" time="18:19:48" level=info msg="Fetching protein inference from /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1" time="18:19:48" level=info msg="Processing peptide identification files" time="18:19:48" level=info msg="Parsing /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_4/interact-CatC_0090_4.pep.xml" time="18:19:48" level=info msg="1+ Charge profile" decoy=0 target=0 time="18:19:48" level=info msg="2+ Charge profile" decoy=30 target=2019 time="18:19:48" level=info msg="3+ Charge profile" decoy=49 target=2849 time="18:19:48" level=info msg="4+ Charge profile" decoy=15 target=811 time="18:19:48" level=info msg="5+ Charge profile" decoy=1 target=28 time="18:19:48" level=info msg="6+ Charge profile" decoy=0 target=0 time="18:19:48" level=info msg="Database search results" ions=1472 peptides=996 psms=5802 time="18:19:48" level=info msg="Converged to 1.00 % FDR with 5626 PSMs" decoy=56 threshold=0.698128 total=5682 time="18:19:48" level=info msg="Converged to 0.98 % FDR with 817 Peptides" decoy=8 threshold=0.972923 total=825 time="18:19:48" level=info msg="Converged to 1.00 % FDR with 1301 Ions" decoy=13 threshold=0.940314 total=1314 time="18:19:48" level=info msg="Protein inference results" decoy=159 target=333 time="18:19:48" level=info msg="Converged to 0.86 % FDR with 233 Proteins" decoy=2 threshold=0.999 total=235 time="18:19:48" level=info msg="Applying sequential FDR estimation" ions=1321 peptides=851 psms=5586 time="18:19:48" level=info msg="Converged to 0.02 % FDR with 5585 PSMs" decoy=1 threshold=0.698779 total=5586 time="18:19:48" level=info msg="Converged to 0.12 % FDR with 850 Peptides" decoy=1 threshold=0.704044 total=851 time="18:19:48" level=info msg="Converged to 0.08 % FDR with 1320 Ions" decoy=1 threshold=0.704044 total=1321 time="18:19:48" level=info msg="Post processing identifications" time="18:19:48" level=info msg="Assigning protein identifications to layers" time="18:19:48" level=info msg="Processing protein inference" time="18:19:48" level=info msg="Synchronizing PSMs and proteins" time="18:19:48" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=1320 peptides=850 proteins=219 psms=5585 time="18:19:48" level=info msg=Saving time="18:19:48" level=info msg=Done Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0000_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0000_1 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor time="18:19:48" level=info msg="Executing Filter v5.1.0" time="18:19:48" level=info msg="Fetching protein inference from /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1" time="18:19:48" level=info msg="Processing peptide identification files" time="18:19:48" level=info msg="Parsing /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0000_1/interact-CatD_0000_1.pep.xml" time="18:19:48" level=info msg="1+ Charge profile" decoy=0 target=0 time="18:19:48" level=info msg="2+ Charge profile" decoy=21 target=1288 time="18:19:48" level=info msg="3+ Charge profile" decoy=41 target=1768 time="18:19:48" level=info msg="4+ Charge profile" decoy=9 target=512 time="18:19:48" level=info msg="5+ Charge profile" decoy=2 target=21 time="18:19:48" level=info msg="6+ Charge profile" decoy=0 target=0 time="18:19:48" level=info msg="Database search results" ions=1350 peptides=905 psms=3662 time="18:19:48" level=info msg="Converged to 0.97 % FDR with 3492 PSMs" decoy=34 threshold=0.744474 total=3526 time="18:19:48" level=info msg="Converged to 0.92 % FDR with 764 Peptides" decoy=7 threshold=0.961424 total=771 time="18:19:48" level=info msg="Converged to 1.00 % FDR with 1204 Ions" decoy=12 threshold=0.940961 total=1216 time="18:19:48" level=info msg="Protein inference results" decoy=159 target=333 time="18:19:48" level=info msg="Converged to 0.86 % FDR with 233 Proteins" decoy=2 threshold=0.999 total=235 time="18:19:48" level=info msg="Applying sequential FDR estimation" ions=1214 peptides=776 psms=3467 time="18:19:48" level=info msg="Converged to 0.00 % FDR with 3467 PSMs" decoy=0 threshold=0.744608 total=3467 time="18:19:48" level=info msg="Converged to 0.00 % FDR with 776 Peptides" decoy=0 threshold=0.811738 total=776 time="18:19:48" level=info msg="Converged to 0.00 % FDR with 1214 Ions" decoy=0 threshold=0.811738 total=1214 time="18:19:48" level=info msg="Post processing identifications" time="18:19:48" level=info msg="Assigning protein identifications to layers" time="18:19:48" level=info msg="Processing protein inference" time="18:19:48" level=info msg="Synchronizing PSMs and proteins" time="18:19:48" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=1214 peptides=776 proteins=215 psms=3467 time="18:19:48" level=info msg=Saving time="18:19:48" level=info msg=Done Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0000_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0000_2 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor time="18:19:49" level=info msg="Executing Filter v5.1.0" time="18:19:49" level=info msg="Fetching protein inference from /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1" time="18:19:49" level=info msg="Processing peptide identification files" time="18:19:49" level=info msg="Parsing /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0000_2/interact-CatD_0000_2.pep.xml" time="18:19:49" level=info msg="1+ Charge profile" decoy=0 target=0 time="18:19:49" level=info msg="2+ Charge profile" decoy=18 target=1301 time="18:19:49" level=info msg="3+ Charge profile" decoy=26 target=1787 time="18:19:49" level=info msg="4+ Charge profile" decoy=11 target=499 time="18:19:49" level=info msg="5+ Charge profile" decoy=1 target=16 time="18:19:49" level=info msg="6+ Charge profile" decoy=0 target=0 time="18:19:49" level=info msg="Database search results" ions=1321 peptides=892 psms=3659 time="18:19:49" level=info msg="Converged to 0.99 % FDR with 3534 PSMs" decoy=35 threshold=0.713762 total=3569 time="18:19:49" level=info msg="Converged to 0.92 % FDR with 765 Peptides" decoy=7 threshold=0.966291 total=772 time="18:19:49" level=info msg="Converged to 1.00 % FDR with 1202 Ions" decoy=12 threshold=0.908335 total=1214 time="18:19:49" level=info msg="Protein inference results" decoy=159 target=333 time="18:19:49" level=info msg="Converged to 0.86 % FDR with 233 Proteins" decoy=2 threshold=0.999 total=235 time="18:19:49" level=info msg="Applying sequential FDR estimation" ions=1206 peptides=783 psms=3498 time="18:19:49" level=info msg="Converged to 0.00 % FDR with 3498 PSMs" decoy=0 threshold=0.713762 total=3498 time="18:19:49" level=info msg="Converged to 0.00 % FDR with 783 Peptides" decoy=0 threshold=0.748689 total=783 time="18:19:49" level=info msg="Converged to 0.00 % FDR with 1206 Ions" decoy=0 threshold=0.745152 total=1206 time="18:19:49" level=info msg="Post processing identifications" time="18:19:49" level=info msg="Assigning protein identifications to layers" time="18:19:49" level=info msg="Processing protein inference" time="18:19:49" level=info msg="Synchronizing PSMs and proteins" time="18:19:49" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=1206 peptides=783 proteins=215 psms=3498 time="18:19:49" level=info msg=Saving time="18:19:49" level=info msg=Done Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_1 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor time="18:19:49" level=info msg="Executing Filter v5.1.0" time="18:19:49" level=info msg="Fetching protein inference from /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1" time="18:19:49" level=info msg="Processing peptide identification files" time="18:19:49" level=info msg="Parsing /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_1/interact-CatD_0015_1.pep.xml" time="18:19:49" level=info msg="1+ Charge profile" decoy=0 target=0 time="18:19:49" level=info msg="2+ Charge profile" decoy=16 target=1423 time="18:19:49" level=info msg="3+ Charge profile" decoy=39 target=1668 time="18:19:49" level=info msg="4+ Charge profile" decoy=12 target=473 time="18:19:49" level=info msg="5+ Charge profile" decoy=0 target=13 time="18:19:49" level=info msg="6+ Charge profile" decoy=0 target=0 time="18:19:49" level=info msg="Database search results" ions=1465 peptides=1025 psms=3644 time="18:19:49" level=info msg="Converged to 0.97 % FDR with 3498 PSMs" decoy=34 threshold=0.740137 total=3532 time="18:19:49" level=info msg="Converged to 0.90 % FDR with 892 Peptides" decoy=8 threshold=0.938952 total=900 time="18:19:49" level=info msg="Converged to 0.97 % FDR with 1337 Ions" decoy=13 threshold=0.895649 total=1350 time="18:19:49" level=info msg="Protein inference results" decoy=159 target=333 time="18:19:49" level=info msg="Converged to 0.86 % FDR with 233 Proteins" decoy=2 threshold=0.999 total=235 time="18:19:49" level=info msg="Applying sequential FDR estimation" ions=1336 peptides=897 psms=3461 time="18:19:49" level=info msg="Converged to 0.03 % FDR with 3460 PSMs" decoy=1 threshold=0.741773 total=3461 time="18:19:49" level=info msg="Converged to 0.11 % FDR with 896 Peptides" decoy=1 threshold=0.814996 total=897 time="18:19:49" level=info msg="Converged to 0.07 % FDR with 1335 Ions" decoy=1 threshold=0.74543 total=1336 time="18:19:49" level=info msg="Post processing identifications" time="18:19:49" level=info msg="Assigning protein identifications to layers" time="18:19:49" level=info msg="Processing protein inference" time="18:19:49" level=info msg="Synchronizing PSMs and proteins" time="18:19:49" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=1335 peptides=896 proteins=228 psms=3460 time="18:19:49" level=info msg=Saving time="18:19:49" level=info msg=Done Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_2 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor time="18:19:49" level=info msg="Executing Filter v5.1.0" time="18:19:49" level=info msg="Fetching protein inference from /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1" time="18:19:49" level=info msg="Processing peptide identification files" time="18:19:49" level=info msg="Parsing /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_2/interact-CatD_0015_2.pep.xml" time="18:19:50" level=info msg="1+ Charge profile" decoy=0 target=0 time="18:19:50" level=info msg="2+ Charge profile" decoy=16 target=1097 time="18:19:50" level=info msg="3+ Charge profile" decoy=34 target=1522 time="18:19:50" level=info msg="4+ Charge profile" decoy=12 target=416 time="18:19:50" level=info msg="5+ Charge profile" decoy=0 target=19 time="18:19:50" level=info msg="6+ Charge profile" decoy=0 target=0 time="18:19:50" level=info msg="Database search results" ions=1282 peptides=871 psms=3116 time="18:19:50" level=info msg="Converged to 0.97 % FDR with 2982 PSMs" decoy=29 threshold=0.735778 total=3011 time="18:19:50" level=info msg="Converged to 0.96 % FDR with 730 Peptides" decoy=7 threshold=0.981934 total=737 time="18:19:50" level=info msg="Converged to 0.95 % FDR with 1162 Ions" decoy=11 threshold=0.935056 total=1173 time="18:19:50" level=info msg="Protein inference results" decoy=159 target=333 time="18:19:50" level=info msg="Converged to 0.86 % FDR with 233 Proteins" decoy=2 threshold=0.999 total=235 time="18:19:50" level=info msg="Applying sequential FDR estimation" ions=1176 peptides=772 psms=2960 time="18:19:50" level=info msg="Converged to 0.00 % FDR with 2960 PSMs" decoy=0 threshold=0.745296 total=2960 time="18:19:50" level=info msg="Converged to 0.00 % FDR with 772 Peptides" decoy=0 threshold=0.772211 total=772 time="18:19:50" level=info msg="Converged to 0.00 % FDR with 1176 Ions" decoy=0 threshold=0.750281 total=1176 time="18:19:50" level=info msg="Post processing identifications" time="18:19:50" level=info msg="Assigning protein identifications to layers" time="18:19:50" level=info msg="Processing protein inference" time="18:19:50" level=info msg="Synchronizing PSMs and proteins" time="18:19:50" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=1176 peptides=772 proteins=225 psms=2960 time="18:19:50" level=info msg=Saving time="18:19:50" level=info msg=Done Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_3 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor time="18:19:50" level=info msg="Executing Filter v5.1.0" time="18:19:50" level=info msg="Fetching protein inference from /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1" time="18:19:50" level=info msg="Processing peptide identification files" time="18:19:50" level=info msg="Parsing /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_3/interact-CatD_0015_3.pep.xml" time="18:19:50" level=info msg="1+ Charge profile" decoy=0 target=0 time="18:19:50" level=info msg="2+ Charge profile" decoy=23 target=1327 time="18:19:50" level=info msg="3+ Charge profile" decoy=50 target=1578 time="18:19:50" level=info msg="4+ Charge profile" decoy=11 target=405 time="18:19:50" level=info msg="5+ Charge profile" decoy=0 target=18 time="18:19:50" level=info msg="6+ Charge profile" decoy=0 target=0 time="18:19:50" level=info msg="Database search results" ions=1389 peptides=959 psms=3412 time="18:19:50" level=info msg="Converged to 0.97 % FDR with 3195 PSMs" decoy=31 threshold=0.813939 total=3226 time="18:19:50" level=info msg="Converged to 0.89 % FDR with 783 Peptides" decoy=7 threshold=0.967534 total=790 time="18:19:50" level=info msg="Converged to 0.99 % FDR with 1214 Ions" decoy=12 threshold=0.936685 total=1226 time="18:19:50" level=info msg="Protein inference results" decoy=159 target=333 time="18:19:50" level=info msg="Converged to 0.86 % FDR with 233 Proteins" decoy=2 threshold=0.999 total=235 time="18:19:50" level=info msg="Applying sequential FDR estimation" ions=1241 peptides=819 psms=3172 time="18:19:50" level=info msg="Converged to 0.00 % FDR with 3172 PSMs" decoy=0 threshold=0.813939 total=3172 time="18:19:50" level=info msg="Converged to 0.00 % FDR with 819 Peptides" decoy=0 threshold=0.813939 total=819 time="18:19:50" level=info msg="Converged to 0.00 % FDR with 1241 Ions" decoy=0 threshold=0.813939 total=1241 time="18:19:50" level=info msg="Post processing identifications" time="18:19:50" level=info msg="Assigning protein identifications to layers" time="18:19:50" level=info msg="Processing protein inference" time="18:19:50" level=info msg="Synchronizing PSMs and proteins" time="18:19:50" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=1241 peptides=819 proteins=221 psms=3172 time="18:19:50" level=info msg=Saving time="18:19:50" level=info msg=Done Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherFilter [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher filter --sequential --prot 0.01 --tag rev_ --pepxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_4 --dbbin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --protxml /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/combined.prot.xml --probin /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1 --razor time="18:19:50" level=info msg="Executing Filter v5.1.0" time="18:19:50" level=info msg="Fetching protein inference from /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1" time="18:19:50" level=info msg="Processing peptide identification files" time="18:19:50" level=info msg="Parsing /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_4/interact-CatD_0015_4.pep.xml" time="18:19:50" level=info msg="1+ Charge profile" decoy=0 target=0 time="18:19:50" level=info msg="2+ Charge profile" decoy=30 target=1521 time="18:19:50" level=info msg="3+ Charge profile" decoy=43 target=1827 time="18:19:50" level=info msg="4+ Charge profile" decoy=20 target=598 time="18:19:50" level=info msg="5+ Charge profile" decoy=1 target=27 time="18:19:50" level=info msg="6+ Charge profile" decoy=0 target=0 time="18:19:50" level=info msg="Database search results" ions=1579 peptides=1096 psms=4067 time="18:19:50" level=info msg="Converged to 0.99 % FDR with 3850 PSMs" decoy=38 threshold=0.733865 total=3888 time="18:19:50" level=info msg="Converged to 0.99 % FDR with 910 Peptides" decoy=9 threshold=0.940948 total=919 time="18:19:50" level=info msg="Converged to 0.93 % FDR with 1394 Ions" decoy=13 threshold=0.896359 total=1407 time="18:19:50" level=info msg="Protein inference results" decoy=159 target=333 time="18:19:50" level=info msg="Converged to 0.86 % FDR with 233 Proteins" decoy=2 threshold=0.999 total=235 time="18:19:50" level=info msg="Applying sequential FDR estimation" ions=1403 peptides=926 psms=3808 time="18:19:50" level=info msg="Converged to 0.03 % FDR with 3807 PSMs" decoy=1 threshold=0.735679 total=3808 time="18:19:50" level=info msg="Converged to 0.11 % FDR with 925 Peptides" decoy=1 threshold=0.73746 total=926 time="18:19:50" level=info msg="Converged to 0.07 % FDR with 1402 Ions" decoy=1 threshold=0.73746 total=1403 time="18:19:50" level=info msg="Post processing identifications" time="18:19:51" level=info msg="Assigning protein identifications to layers" time="18:19:51" level=info msg="Processing protein inference" time="18:19:51" level=info msg="Synchronizing PSMs and proteins" time="18:19:51" level=info msg="Final report numbers after FDR filtering, and post-processing" ions=1402 peptides=925 proteins=225 psms=3807 time="18:19:51" level=info msg=Saving time="18:19:51" level=info msg=Done Process 'PhilosopherFilter' finished, exit code: 0 PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report time="18:19:51" level=info msg="Executing Report v5.1.0" time="18:19:51" level=info msg="Creating reports" time="18:19:51" level=info msg=Done Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report time="18:19:51" level=info msg="Executing Report v5.1.0" time="18:19:51" level=info msg="Creating reports" time="18:19:51" level=info msg=Done Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report time="18:19:51" level=info msg="Executing Report v5.1.0" time="18:19:51" level=info msg="Creating reports" time="18:19:51" level=info msg=Done Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report time="18:19:51" level=info msg="Executing Report v5.1.0" time="18:19:51" level=info msg="Creating reports" time="18:19:51" level=info msg=Done Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report time="18:19:52" level=info msg="Executing Report v5.1.0" time="18:19:52" level=info msg="Creating reports" time="18:19:52" level=info msg=Done Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report time="18:19:52" level=info msg="Executing Report v5.1.0" time="18:19:52" level=info msg="Creating reports" time="18:19:52" level=info msg=Done Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report time="18:19:52" level=info msg="Executing Report v5.1.0" time="18:19:52" level=info msg="Creating reports" time="18:19:52" level=info msg=Done Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report time="18:19:52" level=info msg="Executing Report v5.1.0" time="18:19:52" level=info msg="Creating reports" time="18:19:52" level=info msg=Done Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report time="18:19:52" level=info msg="Executing Report v5.1.0" time="18:19:52" level=info msg="Creating reports" time="18:19:52" level=info msg=Done Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report time="18:19:53" level=info msg="Executing Report v5.1.0" time="18:19:53" level=info msg="Creating reports" time="18:19:53" level=info msg=Done Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report time="18:19:53" level=info msg="Executing Report v5.1.0" time="18:19:53" level=info msg="Creating reports" time="18:19:53" level=info msg=Done Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report time="18:19:53" level=info msg="Executing Report v5.1.0" time="18:19:53" level=info msg="Creating reports" time="18:19:53" level=info msg=Done Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report time="18:19:53" level=info msg="Executing Report v5.1.0" time="18:19:53" level=info msg="Creating reports" time="18:19:53" level=info msg=Done Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report time="18:19:53" level=info msg="Executing Report v5.1.0" time="18:19:53" level=info msg="Creating reports" time="18:19:53" level=info msg=Done Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report time="18:19:54" level=info msg="Executing Report v5.1.0" time="18:19:54" level=info msg="Creating reports" time="18:19:54" level=info msg=Done Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report time="18:19:54" level=info msg="Executing Report v5.1.0" time="18:19:54" level=info msg="Creating reports" time="18:19:54" level=info msg=Done Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report time="18:19:54" level=info msg="Executing Report v5.1.0" time="18:19:54" level=info msg="Creating reports" time="18:19:54" level=info msg=Done Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report time="18:19:54" level=info msg="Executing Report v5.1.0" time="18:19:54" level=info msg="Creating reports" time="18:19:54" level=info msg=Done Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report time="18:19:54" level=info msg="Executing Report v5.1.0" time="18:19:54" level=info msg="Creating reports" time="18:19:54" level=info msg=Done Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report time="18:19:55" level=info msg="Executing Report v5.1.0" time="18:19:55" level=info msg="Creating reports" time="18:19:55" level=info msg=Done Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report time="18:19:55" level=info msg="Executing Report v5.1.0" time="18:19:55" level=info msg="Creating reports" time="18:19:55" level=info msg=Done Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report time="18:19:55" level=info msg="Executing Report v5.1.0" time="18:19:55" level=info msg="Creating reports" time="18:19:55" level=info msg=Done Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0000_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report time="18:19:55" level=info msg="Executing Report v5.1.0" time="18:19:55" level=info msg="Creating reports" time="18:19:55" level=info msg=Done Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0000_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report time="18:19:56" level=info msg="Executing Report v5.1.0" time="18:19:56" level=info msg="Creating reports" time="18:19:56" level=info msg=Done Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report time="18:19:56" level=info msg="Executing Report v5.1.0" time="18:19:56" level=info msg="Creating reports" time="18:19:56" level=info msg=Done Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report time="18:19:56" level=info msg="Executing Report v5.1.0" time="18:19:56" level=info msg="Creating reports" time="18:19:56" level=info msg=Done Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report time="18:19:56" level=info msg="Executing Report v5.1.0" time="18:19:56" level=info msg="Creating reports" time="18:19:56" level=info msg=Done Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report time="18:19:56" level=info msg="Executing Report v5.1.0" time="18:19:56" level=info msg="Creating reports" time="18:19:56" level=info msg=Done Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report time="18:19:57" level=info msg="Executing Report v5.1.0" time="18:19:57" level=info msg="Creating reports" time="18:19:57" level=info msg=Done Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report time="18:19:57" level=info msg="Executing Report v5.1.0" time="18:19:57" level=info msg="Creating reports" time="18:19:57" level=info msg=Done Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report time="18:19:57" level=info msg="Executing Report v5.1.0" time="18:19:57" level=info msg="Creating reports" time="18:19:57" level=info msg=Done Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report time="18:19:57" level=info msg="Executing Report v5.1.0" time="18:19:57" level=info msg="Creating reports" time="18:19:57" level=info msg=Done Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report time="18:19:57" level=info msg="Executing Report v5.1.0" time="18:19:57" level=info msg="Creating reports" time="18:19:57" level=info msg=Done Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report time="18:19:58" level=info msg="Executing Report v5.1.0" time="18:19:58" level=info msg="Creating reports" time="18:19:58" level=info msg=Done Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report time="18:19:58" level=info msg="Executing Report v5.1.0" time="18:19:58" level=info msg="Creating reports" time="18:19:58" level=info msg=Done Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report time="18:19:58" level=info msg="Executing Report v5.1.0" time="18:19:58" level=info msg="Creating reports" time="18:19:58" level=info msg=Done Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report time="18:19:58" level=info msg="Executing Report v5.1.0" time="18:19:58" level=info msg="Creating reports" time="18:19:58" level=info msg=Done Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report time="18:19:58" level=info msg="Executing Report v5.1.0" time="18:19:58" level=info msg="Creating reports" time="18:19:58" level=info msg=Done Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report time="18:19:59" level=info msg="Executing Report v5.1.0" time="18:19:59" level=info msg="Creating reports" time="18:19:59" level=info msg=Done Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report time="18:19:59" level=info msg="Executing Report v5.1.0" time="18:19:59" level=info msg="Creating reports" time="18:19:59" level=info msg=Done Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report time="18:19:59" level=info msg="Executing Report v5.1.0" time="18:19:59" level=info msg="Creating reports" time="18:19:59" level=info msg=Done Process 'PhilosopherReport' finished, exit code: 0 PhilosopherReport [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher report time="18:19:59" level=info msg="Executing Report v5.1.0" time="18:19:59" level=info msg="Creating reports" time="18:19:59" level=info msg=Done Process 'PhilosopherReport' finished, exit code: 0 WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="18:20:00" level=info msg="Executing Workspace v5.1.0" time="18:20:00" level=info msg="Removing workspace" time="18:20:00" level=info msg=Done Process 'WorkspaceClean' finished, exit code: 0 WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="18:20:00" level=info msg="Executing Workspace v5.1.0" time="18:20:00" level=info msg="Removing workspace" time="18:20:00" level=info msg=Done Process 'WorkspaceClean' finished, exit code: 0 WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="18:20:00" level=info msg="Executing Workspace v5.1.0" time="18:20:00" level=info msg="Removing workspace" time="18:20:00" level=info msg=Done Process 'WorkspaceClean' finished, exit code: 0 WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="18:20:00" level=info msg="Executing Workspace v5.1.0" time="18:20:00" level=info msg="Removing workspace" time="18:20:00" level=info msg=Done Process 'WorkspaceClean' finished, exit code: 0 WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="18:20:00" level=info msg="Executing Workspace v5.1.0" time="18:20:00" level=info msg="Removing workspace" time="18:20:00" level=info msg=Done Process 'WorkspaceClean' finished, exit code: 0 WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="18:20:01" level=info msg="Executing Workspace v5.1.0" time="18:20:01" level=info msg="Removing workspace" time="18:20:01" level=info msg=Done Process 'WorkspaceClean' finished, exit code: 0 WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="18:20:01" level=info msg="Executing Workspace v5.1.0" time="18:20:01" level=info msg="Removing workspace" time="18:20:01" level=info msg=Done Process 'WorkspaceClean' finished, exit code: 0 WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="18:20:01" level=info msg="Executing Workspace v5.1.0" time="18:20:01" level=info msg="Removing workspace" time="18:20:01" level=info msg=Done Process 'WorkspaceClean' finished, exit code: 0 WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="18:20:01" level=info msg="Executing Workspace v5.1.0" time="18:20:01" level=info msg="Removing workspace" time="18:20:01" level=info msg=Done Process 'WorkspaceClean' finished, exit code: 0 WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="18:20:01" level=info msg="Executing Workspace v5.1.0" time="18:20:01" level=info msg="Removing workspace" time="18:20:01" level=info msg=Done Process 'WorkspaceClean' finished, exit code: 0 WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="18:20:02" level=info msg="Executing Workspace v5.1.0" time="18:20:02" level=info msg="Removing workspace" time="18:20:02" level=info msg=Done Process 'WorkspaceClean' finished, exit code: 0 WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="18:20:02" level=info msg="Executing Workspace v5.1.0" time="18:20:02" level=info msg="Removing workspace" time="18:20:02" level=info msg=Done Process 'WorkspaceClean' finished, exit code: 0 WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="18:20:02" level=info msg="Executing Workspace v5.1.0" time="18:20:02" level=info msg="Removing workspace" time="18:20:02" level=info msg=Done Process 'WorkspaceClean' finished, exit code: 0 WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="18:20:02" level=info msg="Executing Workspace v5.1.0" time="18:20:02" level=info msg="Removing workspace" time="18:20:02" level=info msg=Done Process 'WorkspaceClean' finished, exit code: 0 WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="18:20:02" level=info msg="Executing Workspace v5.1.0" time="18:20:02" level=info msg="Removing workspace" time="18:20:02" level=info msg=Done Process 'WorkspaceClean' finished, exit code: 0 WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="18:20:03" level=info msg="Executing Workspace v5.1.0" time="18:20:03" level=info msg="Removing workspace" time="18:20:03" level=info msg=Done Process 'WorkspaceClean' finished, exit code: 0 WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="18:20:03" level=info msg="Executing Workspace v5.1.0" time="18:20:03" level=info msg="Removing workspace" time="18:20:03" level=info msg=Done Process 'WorkspaceClean' finished, exit code: 0 WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="18:20:03" level=info msg="Executing Workspace v5.1.0" time="18:20:03" level=info msg="Removing workspace" time="18:20:03" level=info msg=Done Process 'WorkspaceClean' finished, exit code: 0 WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="18:20:03" level=info msg="Executing Workspace v5.1.0" time="18:20:03" level=info msg="Removing workspace" time="18:20:03" level=info msg=Done Process 'WorkspaceClean' finished, exit code: 0 WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="18:20:03" level=info msg="Executing Workspace v5.1.0" time="18:20:03" level=info msg="Removing workspace" time="18:20:03" level=info msg=Done Process 'WorkspaceClean' finished, exit code: 0 WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="18:20:04" level=info msg="Executing Workspace v5.1.0" time="18:20:04" level=info msg="Removing workspace" time="18:20:04" level=info msg=Done Process 'WorkspaceClean' finished, exit code: 0 WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="18:20:04" level=info msg="Executing Workspace v5.1.0" time="18:20:04" level=info msg="Removing workspace" time="18:20:04" level=info msg=Done Process 'WorkspaceClean' finished, exit code: 0 WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0000_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="18:20:04" level=info msg="Executing Workspace v5.1.0" time="18:20:04" level=info msg="Removing workspace" time="18:20:04" level=info msg=Done Process 'WorkspaceClean' finished, exit code: 0 WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0000_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="18:20:04" level=info msg="Executing Workspace v5.1.0" time="18:20:04" level=info msg="Removing workspace" time="18:20:04" level=info msg=Done Process 'WorkspaceClean' finished, exit code: 0 WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="18:20:04" level=info msg="Executing Workspace v5.1.0" time="18:20:04" level=info msg="Removing workspace" time="18:20:04" level=info msg=Done Process 'WorkspaceClean' finished, exit code: 0 WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="18:20:05" level=info msg="Executing Workspace v5.1.0" time="18:20:05" level=info msg="Removing workspace" time="18:20:05" level=info msg=Done Process 'WorkspaceClean' finished, exit code: 0 WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="18:20:05" level=info msg="Executing Workspace v5.1.0" time="18:20:05" level=info msg="Removing workspace" time="18:20:05" level=info msg=Done Process 'WorkspaceClean' finished, exit code: 0 WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="18:20:05" level=info msg="Executing Workspace v5.1.0" time="18:20:05" level=info msg="Removing workspace" time="18:20:05" level=info msg=Done Process 'WorkspaceClean' finished, exit code: 0 WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="18:20:05" level=info msg="Executing Workspace v5.1.0" time="18:20:05" level=info msg="Removing workspace" time="18:20:05" level=info msg=Done Process 'WorkspaceClean' finished, exit code: 0 WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="18:20:05" level=info msg="Executing Workspace v5.1.0" time="18:20:05" level=info msg="Removing workspace" time="18:20:05" level=info msg=Done Process 'WorkspaceClean' finished, exit code: 0 WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="18:20:06" level=info msg="Executing Workspace v5.1.0" time="18:20:06" level=info msg="Removing workspace" time="18:20:06" level=info msg=Done Process 'WorkspaceClean' finished, exit code: 0 WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="18:20:06" level=info msg="Executing Workspace v5.1.0" time="18:20:06" level=info msg="Removing workspace" time="18:20:06" level=info msg=Done Process 'WorkspaceClean' finished, exit code: 0 WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="18:20:06" level=info msg="Executing Workspace v5.1.0" time="18:20:06" level=info msg="Removing workspace" time="18:20:06" level=info msg=Done Process 'WorkspaceClean' finished, exit code: 0 WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="18:20:06" level=info msg="Executing Workspace v5.1.0" time="18:20:06" level=info msg="Removing workspace" time="18:20:06" level=info msg=Done Process 'WorkspaceClean' finished, exit code: 0 WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="18:20:06" level=info msg="Executing Workspace v5.1.0" time="18:20:06" level=info msg="Removing workspace" time="18:20:06" level=info msg=Done Process 'WorkspaceClean' finished, exit code: 0 WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="18:20:07" level=info msg="Executing Workspace v5.1.0" time="18:20:07" level=info msg="Removing workspace" time="18:20:07" level=info msg=Done Process 'WorkspaceClean' finished, exit code: 0 WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_4] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="18:20:07" level=info msg="Executing Workspace v5.1.0" time="18:20:07" level=info msg="Removing workspace" time="18:20:07" level=info msg=Done Process 'WorkspaceClean' finished, exit code: 0 WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="18:20:07" level=info msg="Executing Workspace v5.1.0" time="18:20:07" level=info msg="Removing workspace" time="18:20:07" level=info msg=Done Process 'WorkspaceClean' finished, exit code: 0 WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="18:20:07" level=info msg="Executing Workspace v5.1.0" time="18:20:07" level=info msg="Removing workspace" time="18:20:07" level=info msg=Done Process 'WorkspaceClean' finished, exit code: 0 WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="18:20:07" level=info msg="Executing Workspace v5.1.0" time="18:20:07" level=info msg="Removing workspace" time="18:20:07" level=info msg=Done Process 'WorkspaceClean' finished, exit code: 0 WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_2] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="18:20:08" level=info msg="Executing Workspace v5.1.0" time="18:20:08" level=info msg="Removing workspace" time="18:20:08" level=info msg=Done Process 'WorkspaceClean' finished, exit code: 0 WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="18:20:08" level=info msg="Executing Workspace v5.1.0" time="18:20:08" level=info msg="Removing workspace" time="18:20:08" level=info msg=Done Process 'WorkspaceClean' finished, exit code: 0 WorkspaceClean [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_1] /home/nanopore-catalyst/fragpipe/tools/philosopher_v5.1.0_linux_amd64/philosopher workspace --clean --nocheck time="18:20:08" level=info msg="Executing Workspace v5.1.0" time="18:20:08" level=info msg="Removing workspace" time="18:20:08" level=info msg=Done Process 'WorkspaceClean' finished, exit code: 0 IonQuant [Work dir: /home/nanopore-catalyst/HDD/mspms/fragpipe_out3] java -Xmx56G -Dlibs.bruker.dir=/home/nanopore-catalyst/fragpipe/tools/MSFragger-4.0/ext/bruker -Dlibs.thermo.dir=/home/nanopore-catalyst/fragpipe/tools/MSFragger-4.0/ext/thermo -cp /home/nanopore-catalyst/fragpipe/tools/jfreechart-1.5.3.jar:/home/nanopore-catalyst/fragpipe/tools/batmass-io-1.30.0.jar:/home/nanopore-catalyst/fragpipe/tools/IonQuant-1.10.12.jar ionquant.IonQuant --threads 23 --perform-ms1quant 1 --perform-isoquant 0 --isotol 20.0 --isolevel 2 --isotype tmt10 --ionmobility 0 --site-reports 1 --minexps 1 --mbr 1 --maxlfq 1 --requantify 1 --mztol 10 --imtol 0.05 --rttol 0.4 --mbrmincorr 0 --mbrrttol 1 --mbrimtol 0.05 --mbrtoprun 15 --ionfdr 0.01 --proteinfdr 1 --peptidefdr 1 --normalization 1 --minisotopes 2 --minscans 3 --writeindex 0 --tp 0 --minfreq 0 --minions 2 --locprob 0.75 --uniqueness 0 --multidir . --filelist /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/filelist_ionquant.txt --modlist /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/modmasses_ionquant.txt IonQuant version IonQuant-1.10.12 Batmass-IO version 1.30.0 timsdata library version timsdata-2-21-0-4 (c) University of Michigan System OS: Linux, Architecture: amd64 Java Info: 11.0.23, OpenJDK 64-Bit Server VM, Ubuntu JVM started with 56 GB memory 2024-09-16 18:20:08 [INFO] - Collecting variable modifications from all psm.tsv files... 2024-09-16 18:20:09 [INFO] - Loading and indexing all psm.tsv files... 2024-09-16 18:20:09 [INFO] - Collecting all compensation voltages if applicable... 2024-09-16 18:20:12 [INFO] - Parameters: 2024-09-16 18:20:12 [INFO] - perform-ms1quant = 1 2024-09-16 18:20:12 [INFO] - perform-isoquant = 0 2024-09-16 18:20:12 [INFO] - isotol = 20.0 2024-09-16 18:20:12 [INFO] - isolevel = 2 2024-09-16 18:20:12 [INFO] - isotype = tmt10 2024-09-16 18:20:12 [INFO] - site-reports = 1 2024-09-16 18:20:12 [INFO] - threads = 23 2024-09-16 18:20:12 [INFO] - mztol = 10.0 2024-09-16 18:20:12 [INFO] - rttol = 0.4 2024-09-16 18:20:12 [INFO] - imtol = 0.05 2024-09-16 18:20:12 [INFO] - minisotopes = 2 2024-09-16 18:20:12 [INFO] - minscans = 3 2024-09-16 18:20:12 [INFO] - psm = /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_1/psm.tsv 2024-09-16 18:20:12 [INFO] - psm = /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_2/psm.tsv 2024-09-16 18:20:12 [INFO] - psm = /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_3/psm.tsv 2024-09-16 18:20:12 [INFO] - psm = /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0000_4/psm.tsv 2024-09-16 18:20:12 [INFO] - psm = /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_1/psm.tsv 2024-09-16 18:20:12 [INFO] - psm = /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_2/psm.tsv 2024-09-16 18:20:12 [INFO] - psm = /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_3/psm.tsv 2024-09-16 18:20:12 [INFO] - psm = /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0030_4/psm.tsv 2024-09-16 18:20:12 [INFO] - psm = /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_1/psm.tsv 2024-09-16 18:20:12 [INFO] - psm = /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_2/psm.tsv 2024-09-16 18:20:12 [INFO] - psm = /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_3/psm.tsv 2024-09-16 18:20:12 [INFO] - psm = /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatA_0090_4/psm.tsv 2024-09-16 18:20:12 [INFO] - psm = /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_1/psm.tsv 2024-09-16 18:20:12 [INFO] - psm = /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_2/psm.tsv 2024-09-16 18:20:12 [INFO] - psm = /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_3/psm.tsv 2024-09-16 18:20:12 [INFO] - psm = /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0000_4/psm.tsv 2024-09-16 18:20:12 [INFO] - psm = /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_1/psm.tsv 2024-09-16 18:20:12 [INFO] - psm = /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_2/psm.tsv 2024-09-16 18:20:12 [INFO] - psm = /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_3/psm.tsv 2024-09-16 18:20:12 [INFO] - psm = /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0015_4/psm.tsv 2024-09-16 18:20:12 [INFO] - psm = /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_1/psm.tsv 2024-09-16 18:20:12 [INFO] - psm = /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_2/psm.tsv 2024-09-16 18:20:12 [INFO] - psm = /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_3/psm.tsv 2024-09-16 18:20:12 [INFO] - psm = /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatB_0060_4/psm.tsv 2024-09-16 18:20:12 [INFO] - psm = /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_1/psm.tsv 2024-09-16 18:20:12 [INFO] - psm = /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_2/psm.tsv 2024-09-16 18:20:12 [INFO] - psm = /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_3/psm.tsv 2024-09-16 18:20:12 [INFO] - psm = /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0000_4/psm.tsv 2024-09-16 18:20:12 [INFO] - psm = /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_1/psm.tsv 2024-09-16 18:20:12 [INFO] - psm = /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_2/psm.tsv 2024-09-16 18:20:12 [INFO] - psm = /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_3/psm.tsv 2024-09-16 18:20:12 [INFO] - psm = /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0030_4/psm.tsv 2024-09-16 18:20:12 [INFO] - psm = /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_1/psm.tsv 2024-09-16 18:20:12 [INFO] - psm = /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_2/psm.tsv 2024-09-16 18:20:12 [INFO] - psm = /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_3/psm.tsv 2024-09-16 18:20:12 [INFO] - psm = /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatC_0090_4/psm.tsv 2024-09-16 18:20:12 [INFO] - psm = /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0000_1/psm.tsv 2024-09-16 18:20:12 [INFO] - psm = /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0000_2/psm.tsv 2024-09-16 18:20:12 [INFO] - psm = /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_1/psm.tsv 2024-09-16 18:20:12 [INFO] - psm = /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_2/psm.tsv 2024-09-16 18:20:12 [INFO] - psm = /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_3/psm.tsv 2024-09-16 18:20:12 [INFO] - psm = /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/CatD_0015_4/psm.tsv 2024-09-16 18:20:12 [INFO] - multidir = /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/./ 2024-09-16 18:20:12 [INFO] - excludemods = 2024-09-16 18:20:12 [INFO] - minions = 2 2024-09-16 18:20:12 [INFO] - maxlfq = 1 2024-09-16 18:20:12 [INFO] - ibaq = 0 2024-09-16 18:20:12 [INFO] - normalization = 1 2024-09-16 18:20:12 [INFO] - minexps = 1 2024-09-16 18:20:12 [INFO] - minfreq = 0.0 2024-09-16 18:20:12 [INFO] - tp = 0 2024-09-16 18:20:12 [INFO] - mbr = 1 2024-09-16 18:20:12 [INFO] - mbrrttol = 1.0 2024-09-16 18:20:12 [INFO] - mbrimtol = 0.05 2024-09-16 18:20:12 [INFO] - mbrtoprun = 15 2024-09-16 18:20:12 [INFO] - mbrmincorr = 0.0 2024-09-16 18:20:12 [INFO] - ionmobility = 0 2024-09-16 18:20:12 [INFO] - ionfdr = 0.01 2024-09-16 18:20:12 [INFO] - peptidefdr = 1.0 2024-09-16 18:20:12 [INFO] - proteinfdr = 1.0 2024-09-16 18:20:12 [INFO] - light = 2024-09-16 18:20:12 [INFO] - medium = 2024-09-16 18:20:12 [INFO] - heavy = 2024-09-16 18:20:12 [INFO] - requantify = 0 2024-09-16 18:20:12 [INFO] - writeindex = 0 2024-09-16 18:20:12 [INFO] - locprob = 0.75 2024-09-16 18:20:12 [INFO] - uniqueness = 0 2024-09-16 18:20:12 [INFO] - filelist = /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/filelist_ionquant.txt 2024-09-16 18:20:12 [INFO] - specdir = /home/nanopore-catalyst/HDD/mspms/raw_data 2024-09-16 18:20:12 [INFO] - modlist = /home/nanopore-catalyst/HDD/mspms/fragpipe_out3/modmasses_ionquant.txt 2024-09-16 18:20:12 [INFO] - mod masses: 2024-09-16 18:20:12 [INFO] - 57.02146 2024-09-16 18:20:12 [INFO] - Use each MS2 scan's calculated MZ in peak tracing. 2024-09-16 18:20:12 [INFO] - Loading /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0000_1.raw... 2024-09-16 18:20:17 [INFO] - Building index... 2024-09-16 18:20:17 [INFO] - Writing index to /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0000_1.quantindex 2024-09-16 18:20:18 [INFO] - Quantifying... 2024-09-16 18:20:18 [INFO] - Loading /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0000_2.raw... 2024-09-16 18:20:23 [INFO] - Building index... 2024-09-16 18:20:23 [INFO] - Writing index to /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0000_2.quantindex 2024-09-16 18:20:23 [INFO] - Quantifying... 2024-09-16 18:20:23 [INFO] - Loading /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0000_3.raw... 2024-09-16 18:20:28 [INFO] - Building index... 2024-09-16 18:20:28 [INFO] - Writing index to /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0000_3.quantindex 2024-09-16 18:20:28 [INFO] - Quantifying... 2024-09-16 18:20:28 [INFO] - Loading /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0000_4.raw... 2024-09-16 18:20:33 [INFO] - Building index... 2024-09-16 18:20:33 [INFO] - Writing index to /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0000_4.quantindex 2024-09-16 18:20:33 [INFO] - Quantifying... 2024-09-16 18:20:33 [INFO] - Loading /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0030_1.raw... 2024-09-16 18:20:38 [INFO] - Building index... 2024-09-16 18:20:38 [INFO] - Writing index to /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0030_1.quantindex 2024-09-16 18:20:38 [INFO] - Quantifying... 2024-09-16 18:20:38 [INFO] - Loading /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0030_2.raw... 2024-09-16 18:20:43 [INFO] - Building index... 2024-09-16 18:20:43 [INFO] - Writing index to /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0030_2.quantindex 2024-09-16 18:20:43 [INFO] - Quantifying... 2024-09-16 18:20:43 [INFO] - Loading /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0030_3.raw... 2024-09-16 18:20:47 [INFO] - Building index... 2024-09-16 18:20:48 [INFO] - Writing index to /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0030_3.quantindex 2024-09-16 18:20:48 [INFO] - Quantifying... 2024-09-16 18:20:48 [INFO] - Loading /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0030_4.raw... 2024-09-16 18:20:52 [INFO] - Building index... 2024-09-16 18:20:52 [INFO] - Writing index to /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0030_4.quantindex 2024-09-16 18:20:53 [INFO] - Quantifying... 2024-09-16 18:20:53 [INFO] - Loading /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0090_1.raw... 2024-09-16 18:20:57 [INFO] - Building index... 2024-09-16 18:20:57 [INFO] - Writing index to /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0090_1.quantindex 2024-09-16 18:20:57 [INFO] - Quantifying... 2024-09-16 18:20:57 [INFO] - Loading /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0090_2.raw... 2024-09-16 18:21:02 [INFO] - Building index... 2024-09-16 18:21:02 [INFO] - Writing index to /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0090_2.quantindex 2024-09-16 18:21:02 [INFO] - Quantifying... 2024-09-16 18:21:02 [INFO] - Loading /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0090_3.raw... 2024-09-16 18:21:07 [INFO] - Building index... 2024-09-16 18:21:07 [INFO] - Writing index to /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0090_3.quantindex 2024-09-16 18:21:07 [INFO] - Quantifying... 2024-09-16 18:21:07 [INFO] - Loading /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0090_4.raw... 2024-09-16 18:21:12 [INFO] - Building index... 2024-09-16 18:21:12 [INFO] - Writing index to /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0090_4.quantindex 2024-09-16 18:21:12 [INFO] - Quantifying... 2024-09-16 18:21:13 [INFO] - Loading /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0000_1.raw... 2024-09-16 18:21:17 [INFO] - Building index... 2024-09-16 18:21:18 [INFO] - Writing index to /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0000_1.quantindex 2024-09-16 18:21:18 [INFO] - Quantifying... 2024-09-16 18:21:18 [INFO] - Loading /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0000_2.raw... 2024-09-16 18:21:23 [INFO] - Building index... 2024-09-16 18:21:23 [INFO] - Writing index to /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0000_2.quantindex 2024-09-16 18:21:23 [INFO] - Quantifying... 2024-09-16 18:21:23 [INFO] - Loading /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0000_3.raw... 2024-09-16 18:21:28 [INFO] - Building index... 2024-09-16 18:21:28 [INFO] - Writing index to /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0000_3.quantindex 2024-09-16 18:21:28 [INFO] - Quantifying... 2024-09-16 18:21:28 [INFO] - Loading /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0000_4.raw... 2024-09-16 18:21:33 [INFO] - Building index... 2024-09-16 18:21:33 [INFO] - Writing index to /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0000_4.quantindex 2024-09-16 18:21:33 [INFO] - Quantifying... 2024-09-16 18:21:33 [INFO] - Loading /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0015_1.raw... 2024-09-16 18:21:38 [INFO] - Building index... 2024-09-16 18:21:38 [INFO] - Writing index to /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0015_1.quantindex 2024-09-16 18:21:38 [INFO] - Quantifying... 2024-09-16 18:21:38 [INFO] - Loading /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0015_2.raw... 2024-09-16 18:21:43 [INFO] - Building index... 2024-09-16 18:21:43 [INFO] - Writing index to /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0015_2.quantindex 2024-09-16 18:21:44 [INFO] - Quantifying... 2024-09-16 18:21:44 [INFO] - Loading /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0015_3.raw... 2024-09-16 18:21:49 [INFO] - Building index... 2024-09-16 18:21:49 [INFO] - Writing index to /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0015_3.quantindex 2024-09-16 18:21:49 [INFO] - Quantifying... 2024-09-16 18:21:49 [INFO] - Loading /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0015_4.raw... 2024-09-16 18:21:54 [INFO] - Building index... 2024-09-16 18:21:54 [INFO] - Writing index to /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0015_4.quantindex 2024-09-16 18:21:54 [INFO] - Quantifying... 2024-09-16 18:21:54 [INFO] - Loading /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0060_1.raw... 2024-09-16 18:21:59 [INFO] - Building index... 2024-09-16 18:21:59 [INFO] - Writing index to /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0060_1.quantindex 2024-09-16 18:21:59 [INFO] - Quantifying... 2024-09-16 18:21:59 [INFO] - Loading /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0060_2.raw... 2024-09-16 18:22:04 [INFO] - Building index... 2024-09-16 18:22:04 [INFO] - Writing index to /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0060_2.quantindex 2024-09-16 18:22:04 [INFO] - Quantifying... 2024-09-16 18:22:04 [INFO] - Loading /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0060_3.raw... 2024-09-16 18:22:09 [INFO] - Building index... 2024-09-16 18:22:09 [INFO] - Writing index to /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0060_3.quantindex 2024-09-16 18:22:09 [INFO] - Quantifying... 2024-09-16 18:22:09 [INFO] - Loading /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0060_4.raw... 2024-09-16 18:22:14 [INFO] - Building index... 2024-09-16 18:22:14 [INFO] - Writing index to /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0060_4.quantindex 2024-09-16 18:22:14 [INFO] - Quantifying... 2024-09-16 18:22:14 [INFO] - Loading /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0000_1.raw... 2024-09-16 18:22:19 [INFO] - Building index... 2024-09-16 18:22:19 [INFO] - Writing index to /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0000_1.quantindex 2024-09-16 18:22:19 [INFO] - Quantifying... 2024-09-16 18:22:19 [INFO] - Loading /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0000_2.raw... 2024-09-16 18:22:24 [INFO] - Building index... 2024-09-16 18:22:24 [INFO] - Writing index to /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0000_2.quantindex 2024-09-16 18:22:24 [INFO] - Quantifying... 2024-09-16 18:22:24 [INFO] - Loading /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0000_3.raw... 2024-09-16 18:22:29 [INFO] - Building index... 2024-09-16 18:22:29 [INFO] - Writing index to /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0000_3.quantindex 2024-09-16 18:22:29 [INFO] - Quantifying... 2024-09-16 18:22:29 [INFO] - Loading /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0000_4.raw... 2024-09-16 18:22:34 [INFO] - Building index... 2024-09-16 18:22:34 [INFO] - Writing index to /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0000_4.quantindex 2024-09-16 18:22:34 [INFO] - Quantifying... 2024-09-16 18:22:34 [INFO] - Loading /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0030_1.raw... 2024-09-16 18:22:39 [INFO] - Building index... 2024-09-16 18:22:39 [INFO] - Writing index to /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0030_1.quantindex 2024-09-16 18:22:39 [INFO] - Quantifying... 2024-09-16 18:22:39 [INFO] - Loading /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0030_2.raw... 2024-09-16 18:22:44 [INFO] - Building index... 2024-09-16 18:22:44 [INFO] - Writing index to /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0030_2.quantindex 2024-09-16 18:22:44 [INFO] - Quantifying... 2024-09-16 18:22:44 [INFO] - Loading /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0030_3.raw... 2024-09-16 18:22:48 [INFO] - Building index... 2024-09-16 18:22:49 [INFO] - Writing index to /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0030_3.quantindex 2024-09-16 18:22:49 [INFO] - Quantifying... 2024-09-16 18:22:49 [INFO] - Loading /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0030_4.raw... 2024-09-16 18:22:53 [INFO] - Building index... 2024-09-16 18:22:53 [INFO] - Writing index to /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0030_4.quantindex 2024-09-16 18:22:54 [INFO] - Quantifying... 2024-09-16 18:22:54 [INFO] - Loading /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0090_1.raw... 2024-09-16 18:22:58 [INFO] - Building index... 2024-09-16 18:22:58 [INFO] - Writing index to /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0090_1.quantindex 2024-09-16 18:22:58 [INFO] - Quantifying... 2024-09-16 18:22:58 [INFO] - Loading /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0090_2.raw... 2024-09-16 18:23:03 [INFO] - Building index... 2024-09-16 18:23:03 [INFO] - Writing index to /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0090_2.quantindex 2024-09-16 18:23:03 [INFO] - Quantifying... 2024-09-16 18:23:03 [INFO] - Loading /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0090_3.raw... 2024-09-16 18:23:08 [INFO] - Building index... 2024-09-16 18:23:08 [INFO] - Writing index to /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0090_3.quantindex 2024-09-16 18:23:08 [INFO] - Quantifying... 2024-09-16 18:23:08 [INFO] - Loading /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0090_4.raw... 2024-09-16 18:23:13 [INFO] - Building index... 2024-09-16 18:23:13 [INFO] - Writing index to /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0090_4.quantindex 2024-09-16 18:23:13 [INFO] - Quantifying... 2024-09-16 18:23:13 [INFO] - Loading /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0000_1.raw... 2024-09-16 18:23:17 [INFO] - Building index... 2024-09-16 18:23:17 [INFO] - Writing index to /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0000_1.quantindex 2024-09-16 18:23:17 [INFO] - Quantifying... 2024-09-16 18:23:17 [INFO] - Loading /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0000_2.raw... 2024-09-16 18:23:20 [INFO] - Building index... 2024-09-16 18:23:20 [INFO] - Writing index to /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0000_2.quantindex 2024-09-16 18:23:21 [INFO] - Quantifying... 2024-09-16 18:23:21 [INFO] - Loading /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0015_1.raw... 2024-09-16 18:23:24 [INFO] - Building index... 2024-09-16 18:23:24 [INFO] - Writing index to /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0015_1.quantindex 2024-09-16 18:23:24 [INFO] - Quantifying... 2024-09-16 18:23:24 [INFO] - Loading /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0015_2.raw... 2024-09-16 18:23:28 [INFO] - Building index... 2024-09-16 18:23:28 [INFO] - Writing index to /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0015_2.quantindex 2024-09-16 18:23:28 [INFO] - Quantifying... 2024-09-16 18:23:28 [INFO] - Loading /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0015_3.raw... 2024-09-16 18:23:32 [INFO] - Building index... 2024-09-16 18:23:32 [INFO] - Writing index to /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0015_3.quantindex 2024-09-16 18:23:32 [INFO] - Quantifying... 2024-09-16 18:23:32 [INFO] - Loading /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0015_4.raw... 2024-09-16 18:23:35 [INFO] - Building index... 2024-09-16 18:23:35 [INFO] - Writing index to /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0015_4.quantindex 2024-09-16 18:23:35 [INFO] - Quantifying... 2024-09-16 18:23:35 [INFO] - Updating Philosopher's tables... 2024-09-16 18:23:38 [INFO] - Matching-between-runs: CatA_0000_1... 2024-09-16 18:23:38 [INFO] - Calculating correlations between all other runs... 2024-09-16 18:23:38 [INFO] - Reading index from /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0000_1.quantindex 2024-09-16 18:23:38 [INFO] - Transferring CatA_0000_2... 2024-09-16 18:23:38 [INFO] - Transferring CatA_0000_3... 2024-09-16 18:23:38 [INFO] - Transferring CatA_0000_4... 2024-09-16 18:23:38 [INFO] - Transferring CatC_0000_1... 2024-09-16 18:23:38 [INFO] - Transferring CatC_0000_2... 2024-09-16 18:23:38 [INFO] - Transferring CatC_0000_3... 2024-09-16 18:23:38 [INFO] - Transferring CatC_0000_4... 2024-09-16 18:23:38 [INFO] - Transferring CatC_0030_1... 2024-09-16 18:23:38 [INFO] - Transferring CatC_0030_2... 2024-09-16 18:23:38 [INFO] - Transferring CatC_0030_3... 2024-09-16 18:23:38 [INFO] - Transferring CatC_0030_4... 2024-09-16 18:23:38 [INFO] - Transferring CatC_0090_1... 2024-09-16 18:23:38 [INFO] - Transferring CatC_0090_2... 2024-09-16 18:23:38 [INFO] - Transferring CatC_0090_3... 2024-09-16 18:23:38 [INFO] - Transferring CatC_0090_4... 2024-09-16 18:23:38 [INFO] - Training LDA models for all matched features. 2024-09-16 18:23:38 [INFO] - #{+1} = 406, #{-1} = 34, #{+2} = 1012, #{-2} = 91 2024-09-16 18:23:38 [INFO] - Standardized coefficients: 2024-09-16 18:23:38 [INFO] - log10(intensity): 0.7498363364549707 2024-09-16 18:23:38 [INFO] - log10(KL): -0.44712075709663035 2024-09-16 18:23:38 [INFO] - abs(ppm): -0.431903078706138 2024-09-16 18:23:38 [INFO] - RT diff: -0.3338574033455729 2024-09-16 18:23:38 [INFO] - Fitting a mixture model... 2024-09-16 18:23:39 [INFO] - Matching-between-runs: CatA_0000_2... 2024-09-16 18:23:39 [INFO] - Calculating correlations between all other runs... 2024-09-16 18:23:39 [INFO] - Reading index from /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0000_2.quantindex 2024-09-16 18:23:39 [INFO] - Transferring CatA_0000_1... 2024-09-16 18:23:39 [INFO] - Transferring CatA_0000_3... 2024-09-16 18:23:39 [INFO] - Transferring CatA_0000_4... 2024-09-16 18:23:39 [INFO] - Transferring CatC_0000_1... 2024-09-16 18:23:39 [INFO] - Transferring CatC_0000_2... 2024-09-16 18:23:39 [INFO] - Transferring CatC_0000_3... 2024-09-16 18:23:39 [INFO] - Transferring CatC_0000_4... 2024-09-16 18:23:39 [INFO] - Transferring CatC_0030_1... 2024-09-16 18:23:39 [INFO] - Transferring CatC_0030_2... 2024-09-16 18:23:39 [INFO] - Transferring CatC_0030_3... 2024-09-16 18:23:39 [INFO] - Transferring CatC_0030_4... 2024-09-16 18:23:39 [INFO] - Transferring CatC_0090_1... 2024-09-16 18:23:39 [INFO] - Transferring CatC_0090_2... 2024-09-16 18:23:39 [INFO] - Transferring CatC_0090_3... 2024-09-16 18:23:39 [INFO] - Transferring CatC_0090_4... 2024-09-16 18:23:39 [INFO] - Training LDA models for all matched features. 2024-09-16 18:23:39 [INFO] - #{+1} = 432, #{-1} = 30, #{+2} = 981, #{-2} = 83 2024-09-16 18:23:39 [INFO] - Standardized coefficients: 2024-09-16 18:23:39 [INFO] - log10(intensity): 0.6943584207294573 2024-09-16 18:23:39 [INFO] - log10(KL): -0.3736003991879667 2024-09-16 18:23:39 [INFO] - abs(ppm): -0.5678428106208075 2024-09-16 18:23:39 [INFO] - RT diff: -0.319526077907731 2024-09-16 18:23:39 [INFO] - Fitting a mixture model... 2024-09-16 18:23:39 [INFO] - Matching-between-runs: CatA_0000_3... 2024-09-16 18:23:39 [INFO] - Calculating correlations between all other runs... 2024-09-16 18:23:39 [INFO] - Reading index from /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0000_3.quantindex 2024-09-16 18:23:39 [INFO] - Transferring CatA_0000_1... 2024-09-16 18:23:39 [INFO] - Transferring CatA_0000_2... 2024-09-16 18:23:39 [INFO] - Transferring CatA_0000_4... 2024-09-16 18:23:39 [INFO] - Transferring CatC_0000_1... 2024-09-16 18:23:40 [INFO] - Transferring CatC_0000_2... 2024-09-16 18:23:40 [INFO] - Transferring CatC_0000_3... 2024-09-16 18:23:40 [INFO] - Transferring CatC_0000_4... 2024-09-16 18:23:40 [INFO] - Transferring CatC_0030_1... 2024-09-16 18:23:40 [INFO] - Transferring CatC_0030_2... 2024-09-16 18:23:40 [INFO] - Transferring CatC_0030_3... 2024-09-16 18:23:40 [INFO] - Transferring CatC_0030_4... 2024-09-16 18:23:40 [INFO] - Transferring CatC_0090_1... 2024-09-16 18:23:40 [INFO] - Transferring CatC_0090_2... 2024-09-16 18:23:40 [INFO] - Transferring CatC_0090_3... 2024-09-16 18:23:40 [INFO] - Transferring CatC_0090_4... 2024-09-16 18:23:40 [INFO] - Training LDA models for all matched features. 2024-09-16 18:23:40 [INFO] - #{+1} = 428, #{-1} = 29, #{+2} = 998, #{-2} = 76 2024-09-16 18:23:40 [INFO] - Standardized coefficients: 2024-09-16 18:23:40 [INFO] - log10(intensity): 0.6686587195981032 2024-09-16 18:23:40 [INFO] - log10(KL): -0.3701663739178586 2024-09-16 18:23:40 [INFO] - abs(ppm): -0.562193052248658 2024-09-16 18:23:40 [INFO] - RT diff: -0.36341239212798265 2024-09-16 18:23:40 [INFO] - Fitting a mixture model... 2024-09-16 18:23:40 [INFO] - Matching-between-runs: CatA_0000_4... 2024-09-16 18:23:40 [INFO] - Calculating correlations between all other runs... 2024-09-16 18:23:40 [INFO] - Reading index from /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0000_4.quantindex 2024-09-16 18:23:40 [INFO] - Transferring CatA_0000_1... 2024-09-16 18:23:40 [INFO] - Transferring CatA_0000_2... 2024-09-16 18:23:40 [INFO] - Transferring CatA_0000_3... 2024-09-16 18:23:40 [INFO] - Transferring CatC_0000_1... 2024-09-16 18:23:40 [INFO] - Transferring CatC_0000_2... 2024-09-16 18:23:40 [INFO] - Transferring CatC_0000_3... 2024-09-16 18:23:40 [INFO] - Transferring CatC_0000_4... 2024-09-16 18:23:40 [INFO] - Transferring CatC_0030_1... 2024-09-16 18:23:40 [INFO] - Transferring CatC_0030_2... 2024-09-16 18:23:40 [INFO] - Transferring CatC_0030_3... 2024-09-16 18:23:40 [INFO] - Transferring CatC_0030_4... 2024-09-16 18:23:40 [INFO] - Transferring CatC_0090_1... 2024-09-16 18:23:40 [INFO] - Transferring CatC_0090_2... 2024-09-16 18:23:40 [INFO] - Transferring CatC_0090_3... 2024-09-16 18:23:40 [INFO] - Transferring CatC_0090_4... 2024-09-16 18:23:40 [INFO] - Training LDA models for all matched features. 2024-09-16 18:23:40 [INFO] - #{+1} = 395, #{-1} = 39, #{+2} = 1013, #{-2} = 95 2024-09-16 18:23:40 [INFO] - Standardized coefficients: 2024-09-16 18:23:40 [INFO] - log10(intensity): 0.5817801988148279 2024-09-16 18:23:40 [INFO] - log10(KL): -0.5493255509119214 2024-09-16 18:23:40 [INFO] - abs(ppm): -0.5841830149076928 2024-09-16 18:23:40 [INFO] - RT diff: -0.13602736664234805 2024-09-16 18:23:40 [INFO] - Fitting a mixture model... 2024-09-16 18:23:40 [INFO] - Matching-between-runs: CatA_0030_1... 2024-09-16 18:23:40 [INFO] - Calculating correlations between all other runs... 2024-09-16 18:23:40 [INFO] - Reading index from /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0030_1.quantindex 2024-09-16 18:23:40 [INFO] - Transferring CatA_0000_1... 2024-09-16 18:23:40 [INFO] - Transferring CatA_0000_2... 2024-09-16 18:23:40 [INFO] - Transferring CatA_0000_3... 2024-09-16 18:23:40 [INFO] - Transferring CatA_0000_4... 2024-09-16 18:23:40 [INFO] - Transferring CatA_0030_2... 2024-09-16 18:23:40 [INFO] - Transferring CatA_0030_3... 2024-09-16 18:23:40 [INFO] - Transferring CatA_0030_4... 2024-09-16 18:23:40 [INFO] - Transferring CatA_0090_1... 2024-09-16 18:23:40 [INFO] - Transferring CatA_0090_2... 2024-09-16 18:23:40 [INFO] - Transferring CatA_0090_3... 2024-09-16 18:23:40 [INFO] - Transferring CatA_0090_4... 2024-09-16 18:23:40 [INFO] - Transferring CatC_0000_1... 2024-09-16 18:23:40 [INFO] - Transferring CatC_0000_2... 2024-09-16 18:23:40 [INFO] - Transferring CatC_0000_3... 2024-09-16 18:23:40 [INFO] - Transferring CatC_0000_4... 2024-09-16 18:23:40 [INFO] - Training LDA models for all matched features. 2024-09-16 18:23:40 [INFO] - #{+1} = 495, #{-1} = 40, #{+2} = 1224, #{-2} = 114 2024-09-16 18:23:40 [INFO] - Standardized coefficients: 2024-09-16 18:23:40 [INFO] - log10(intensity): 0.721994858565759 2024-09-16 18:23:40 [INFO] - log10(KL): -0.2756620181105194 2024-09-16 18:23:40 [INFO] - abs(ppm): -0.5320920368807885 2024-09-16 18:23:40 [INFO] - RT diff: -0.3458495919672292 2024-09-16 18:23:40 [INFO] - Fitting a mixture model... 2024-09-16 18:23:41 [INFO] - Matching-between-runs: CatA_0030_2... 2024-09-16 18:23:41 [INFO] - Calculating correlations between all other runs... 2024-09-16 18:23:41 [INFO] - Reading index from /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0030_2.quantindex 2024-09-16 18:23:41 [INFO] - Transferring CatA_0000_1... 2024-09-16 18:23:41 [INFO] - Transferring CatA_0000_2... 2024-09-16 18:23:41 [INFO] - Transferring CatA_0000_3... 2024-09-16 18:23:41 [INFO] - Transferring CatA_0000_4... 2024-09-16 18:23:41 [INFO] - Transferring CatA_0030_1... 2024-09-16 18:23:41 [INFO] - Transferring CatA_0030_3... 2024-09-16 18:23:41 [INFO] - Transferring CatA_0030_4... 2024-09-16 18:23:41 [INFO] - Transferring CatA_0090_1... 2024-09-16 18:23:41 [INFO] - Transferring CatA_0090_2... 2024-09-16 18:23:41 [INFO] - Transferring CatA_0090_3... 2024-09-16 18:23:41 [INFO] - Transferring CatA_0090_4... 2024-09-16 18:23:41 [INFO] - Transferring CatC_0000_1... 2024-09-16 18:23:41 [INFO] - Transferring CatC_0000_2... 2024-09-16 18:23:41 [INFO] - Transferring CatC_0000_3... 2024-09-16 18:23:41 [INFO] - Transferring CatC_0000_4... 2024-09-16 18:23:41 [INFO] - Training LDA models for all matched features. 2024-09-16 18:23:41 [INFO] - #{+1} = 526, #{-1} = 50, #{+2} = 1169, #{-2} = 123 2024-09-16 18:23:41 [INFO] - Standardized coefficients: 2024-09-16 18:23:41 [INFO] - log10(intensity): 0.7548463096774647 2024-09-16 18:23:41 [INFO] - log10(KL): -0.3862185757435207 2024-09-16 18:23:41 [INFO] - abs(ppm): -0.5469195316345448 2024-09-16 18:23:41 [INFO] - RT diff: -0.20413385766967634 2024-09-16 18:23:41 [INFO] - Fitting a mixture model... 2024-09-16 18:23:41 [INFO] - Matching-between-runs: CatA_0030_3... 2024-09-16 18:23:41 [INFO] - Calculating correlations between all other runs... 2024-09-16 18:23:41 [INFO] - Reading index from /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0030_3.quantindex 2024-09-16 18:23:41 [INFO] - Transferring CatA_0000_1... 2024-09-16 18:23:41 [INFO] - Transferring CatA_0000_2... 2024-09-16 18:23:41 [INFO] - Transferring CatA_0000_3... 2024-09-16 18:23:41 [INFO] - Transferring CatA_0000_4... 2024-09-16 18:23:41 [INFO] - Transferring CatA_0030_1... 2024-09-16 18:23:41 [INFO] - Transferring CatA_0030_2... 2024-09-16 18:23:41 [INFO] - Transferring CatA_0030_4... 2024-09-16 18:23:41 [INFO] - Transferring CatA_0090_1... 2024-09-16 18:23:41 [INFO] - Transferring CatA_0090_2... 2024-09-16 18:23:41 [INFO] - Transferring CatA_0090_3... 2024-09-16 18:23:41 [INFO] - Transferring CatA_0090_4... 2024-09-16 18:23:41 [INFO] - Transferring CatC_0000_1... 2024-09-16 18:23:41 [INFO] - Transferring CatC_0000_2... 2024-09-16 18:23:41 [INFO] - Transferring CatC_0000_3... 2024-09-16 18:23:41 [INFO] - Transferring CatC_0000_4... 2024-09-16 18:23:41 [INFO] - Training LDA models for all matched features. 2024-09-16 18:23:41 [INFO] - #{+1} = 534, #{-1} = 57, #{+2} = 1173, #{-2} = 116 2024-09-16 18:23:41 [INFO] - Standardized coefficients: 2024-09-16 18:23:41 [INFO] - log10(intensity): 0.5618087502499229 2024-09-16 18:23:41 [INFO] - log10(KL): -0.6134467963092141 2024-09-16 18:23:41 [INFO] - abs(ppm): -0.48687341262955597 2024-09-16 18:23:41 [INFO] - RT diff: -0.27432836684017997 2024-09-16 18:23:41 [INFO] - Fitting a mixture model... 2024-09-16 18:23:41 [INFO] - Matching-between-runs: CatA_0030_4... 2024-09-16 18:23:41 [INFO] - Calculating correlations between all other runs... 2024-09-16 18:23:41 [INFO] - Reading index from /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0030_4.quantindex 2024-09-16 18:23:41 [INFO] - Transferring CatA_0000_1... 2024-09-16 18:23:41 [INFO] - Transferring CatA_0000_2... 2024-09-16 18:23:41 [INFO] - Transferring CatA_0000_3... 2024-09-16 18:23:41 [INFO] - Transferring CatA_0000_4... 2024-09-16 18:23:41 [INFO] - Transferring CatA_0030_1... 2024-09-16 18:23:41 [INFO] - Transferring CatA_0030_2... 2024-09-16 18:23:41 [INFO] - Transferring CatA_0030_3... 2024-09-16 18:23:41 [INFO] - Transferring CatA_0090_1... 2024-09-16 18:23:42 [INFO] - Transferring CatA_0090_2... 2024-09-16 18:23:42 [INFO] - Transferring CatA_0090_3... 2024-09-16 18:23:42 [INFO] - Transferring CatA_0090_4... 2024-09-16 18:23:42 [INFO] - Transferring CatC_0000_1... 2024-09-16 18:23:42 [INFO] - Transferring CatC_0000_2... 2024-09-16 18:23:42 [INFO] - Transferring CatC_0000_3... 2024-09-16 18:23:42 [INFO] - Transferring CatC_0000_4... 2024-09-16 18:23:42 [INFO] - Training LDA models for all matched features. 2024-09-16 18:23:42 [INFO] - #{+1} = 462, #{-1} = 28, #{+2} = 1218, #{-2} = 122 2024-09-16 18:23:42 [INFO] - Standardized coefficients: 2024-09-16 18:23:42 [INFO] - log10(intensity): 0.5829089254442975 2024-09-16 18:23:42 [INFO] - log10(KL): -0.4795724834544712 2024-09-16 18:23:42 [INFO] - abs(ppm): -0.6184695966211087 2024-09-16 18:23:42 [INFO] - RT diff: -0.253276138848833 2024-09-16 18:23:42 [INFO] - Fitting a mixture model... 2024-09-16 18:23:42 [INFO] - Matching-between-runs: CatA_0090_1... 2024-09-16 18:23:42 [INFO] - Calculating correlations between all other runs... 2024-09-16 18:23:42 [INFO] - Reading index from /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0090_1.quantindex 2024-09-16 18:23:42 [INFO] - Transferring CatA_0000_1... 2024-09-16 18:23:42 [INFO] - Transferring CatA_0000_2... 2024-09-16 18:23:42 [INFO] - Transferring CatA_0000_3... 2024-09-16 18:23:42 [INFO] - Transferring CatA_0000_4... 2024-09-16 18:23:42 [INFO] - Transferring CatA_0030_1... 2024-09-16 18:23:42 [INFO] - Transferring CatA_0030_2... 2024-09-16 18:23:42 [INFO] - Transferring CatA_0030_3... 2024-09-16 18:23:42 [INFO] - Transferring CatA_0030_4... 2024-09-16 18:23:42 [INFO] - Transferring CatA_0090_2... 2024-09-16 18:23:42 [INFO] - Transferring CatA_0090_3... 2024-09-16 18:23:42 [INFO] - Transferring CatA_0090_4... 2024-09-16 18:23:42 [INFO] - Transferring CatC_0000_1... 2024-09-16 18:23:42 [INFO] - Transferring CatC_0000_2... 2024-09-16 18:23:42 [INFO] - Transferring CatC_0000_3... 2024-09-16 18:23:42 [INFO] - Transferring CatC_0000_4... 2024-09-16 18:23:42 [INFO] - Training LDA models for all matched features. 2024-09-16 18:23:42 [INFO] - #{+1} = 470, #{-1} = 48, #{+2} = 1212, #{-2} = 118 2024-09-16 18:23:42 [INFO] - Standardized coefficients: 2024-09-16 18:23:42 [INFO] - log10(intensity): 0.7336258831931641 2024-09-16 18:23:42 [INFO] - log10(KL): -0.3191312880224411 2024-09-16 18:23:42 [INFO] - abs(ppm): -0.5316548087767285 2024-09-16 18:23:42 [INFO] - RT diff: -0.27801339683326043 2024-09-16 18:23:42 [INFO] - Fitting a mixture model... 2024-09-16 18:23:42 [INFO] - Matching-between-runs: CatA_0090_2... 2024-09-16 18:23:42 [INFO] - Calculating correlations between all other runs... 2024-09-16 18:23:42 [INFO] - Reading index from /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0090_2.quantindex 2024-09-16 18:23:42 [INFO] - Transferring CatA_0000_1... 2024-09-16 18:23:42 [INFO] - Transferring CatA_0000_2... 2024-09-16 18:23:42 [INFO] - Transferring CatA_0000_3... 2024-09-16 18:23:42 [INFO] - Transferring CatA_0000_4... 2024-09-16 18:23:42 [INFO] - Transferring CatA_0030_1... 2024-09-16 18:23:42 [INFO] - Transferring CatA_0030_2... 2024-09-16 18:23:42 [INFO] - Transferring CatA_0030_3... 2024-09-16 18:23:42 [INFO] - Transferring CatA_0030_4... 2024-09-16 18:23:42 [INFO] - Transferring CatA_0090_1... 2024-09-16 18:23:42 [INFO] - Transferring CatA_0090_3... 2024-09-16 18:23:42 [INFO] - Transferring CatA_0090_4... 2024-09-16 18:23:42 [INFO] - Transferring CatC_0000_1... 2024-09-16 18:23:42 [INFO] - Transferring CatC_0000_2... 2024-09-16 18:23:42 [INFO] - Transferring CatC_0000_3... 2024-09-16 18:23:42 [INFO] - Transferring CatC_0000_4... 2024-09-16 18:23:42 [INFO] - Training LDA models for all matched features. 2024-09-16 18:23:42 [INFO] - #{+1} = 491, #{-1} = 53, #{+2} = 1206, #{-2} = 114 2024-09-16 18:23:42 [INFO] - Standardized coefficients: 2024-09-16 18:23:42 [INFO] - log10(intensity): 0.8279941835292547 2024-09-16 18:23:42 [INFO] - log10(KL): -0.23530581499952438 2024-09-16 18:23:42 [INFO] - abs(ppm): -0.41974940805166494 2024-09-16 18:23:42 [INFO] - RT diff: -0.28786670510743245 2024-09-16 18:23:42 [INFO] - Fitting a mixture model... 2024-09-16 18:23:42 [INFO] - Matching-between-runs: CatA_0090_3... 2024-09-16 18:23:42 [INFO] - Calculating correlations between all other runs... 2024-09-16 18:23:43 [INFO] - Reading index from /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0090_3.quantindex 2024-09-16 18:23:43 [INFO] - Transferring CatA_0000_1... 2024-09-16 18:23:43 [INFO] - Transferring CatA_0000_2... 2024-09-16 18:23:43 [INFO] - Transferring CatA_0000_3... 2024-09-16 18:23:43 [INFO] - Transferring CatA_0000_4... 2024-09-16 18:23:43 [INFO] - Transferring CatA_0030_1... 2024-09-16 18:23:43 [INFO] - Transferring CatA_0030_2... 2024-09-16 18:23:43 [INFO] - Transferring CatA_0030_3... 2024-09-16 18:23:43 [INFO] - Transferring CatA_0030_4... 2024-09-16 18:23:43 [INFO] - Transferring CatA_0090_1... 2024-09-16 18:23:43 [INFO] - Transferring CatA_0090_2... 2024-09-16 18:23:43 [INFO] - Transferring CatA_0090_4... 2024-09-16 18:23:43 [INFO] - Transferring CatC_0000_1... 2024-09-16 18:23:43 [INFO] - Transferring CatC_0000_2... 2024-09-16 18:23:43 [INFO] - Transferring CatC_0000_3... 2024-09-16 18:23:43 [INFO] - Transferring CatC_0000_4... 2024-09-16 18:23:43 [INFO] - Training LDA models for all matched features. 2024-09-16 18:23:43 [INFO] - #{+1} = 478, #{-1} = 57, #{+2} = 1179, #{-2} = 105 2024-09-16 18:23:43 [INFO] - Standardized coefficients: 2024-09-16 18:23:43 [INFO] - log10(intensity): 0.7031021488916351 2024-09-16 18:23:43 [INFO] - log10(KL): -0.38874469224333613 2024-09-16 18:23:43 [INFO] - abs(ppm): -0.5225160808577476 2024-09-16 18:23:43 [INFO] - RT diff: -0.3381936098917348 2024-09-16 18:23:43 [INFO] - Fitting a mixture model... 2024-09-16 18:23:43 [INFO] - Matching-between-runs: CatA_0090_4... 2024-09-16 18:23:43 [INFO] - Calculating correlations between all other runs... 2024-09-16 18:23:43 [INFO] - Reading index from /home/nanopore-catalyst/HDD/mspms/raw_data/CatA_0090_4.quantindex 2024-09-16 18:23:43 [INFO] - Transferring CatA_0000_1... 2024-09-16 18:23:43 [INFO] - Transferring CatA_0000_2... 2024-09-16 18:23:43 [INFO] - Transferring CatA_0000_3... 2024-09-16 18:23:43 [INFO] - Transferring CatA_0000_4... 2024-09-16 18:23:43 [INFO] - Transferring CatA_0030_1... 2024-09-16 18:23:43 [INFO] - Transferring CatA_0030_2... 2024-09-16 18:23:43 [INFO] - Transferring CatA_0030_3... 2024-09-16 18:23:43 [INFO] - Transferring CatA_0030_4... 2024-09-16 18:23:43 [INFO] - Transferring CatA_0090_1... 2024-09-16 18:23:43 [INFO] - Transferring CatA_0090_2... 2024-09-16 18:23:43 [INFO] - Transferring CatA_0090_3... 2024-09-16 18:23:43 [INFO] - Transferring CatC_0000_1... 2024-09-16 18:23:43 [INFO] - Transferring CatC_0000_2... 2024-09-16 18:23:43 [INFO] - Transferring CatC_0000_3... 2024-09-16 18:23:43 [INFO] - Transferring CatC_0000_4... 2024-09-16 18:23:43 [INFO] - Training LDA models for all matched features. 2024-09-16 18:23:43 [INFO] - #{+1} = 482, #{-1} = 36, #{+2} = 1188, #{-2} = 101 2024-09-16 18:23:43 [INFO] - Standardized coefficients: 2024-09-16 18:23:43 [INFO] - log10(intensity): 0.6822400002064072 2024-09-16 18:23:43 [INFO] - log10(KL): -0.2865318126087679 2024-09-16 18:23:43 [INFO] - abs(ppm): -0.6242972270277581 2024-09-16 18:23:43 [INFO] - RT diff: -0.3153226413777634 2024-09-16 18:23:43 [INFO] - Fitting a mixture model... 2024-09-16 18:23:43 [INFO] - Matching-between-runs: CatB_0000_1... 2024-09-16 18:23:43 [INFO] - Calculating correlations between all other runs... 2024-09-16 18:23:43 [INFO] - Reading index from /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0000_1.quantindex 2024-09-16 18:23:43 [INFO] - Transferring CatA_0000_1... 2024-09-16 18:23:43 [INFO] - Transferring CatA_0000_4... 2024-09-16 18:23:43 [INFO] - Transferring CatB_0000_2... 2024-09-16 18:23:43 [INFO] - Transferring CatB_0000_3... 2024-09-16 18:23:43 [INFO] - Transferring CatB_0000_4... 2024-09-16 18:23:43 [INFO] - Transferring CatB_0015_1... 2024-09-16 18:23:43 [INFO] - Transferring CatB_0015_2... 2024-09-16 18:23:43 [INFO] - Transferring CatB_0015_3... 2024-09-16 18:23:43 [INFO] - Transferring CatB_0015_4... 2024-09-16 18:23:43 [INFO] - Transferring CatB_0060_1... 2024-09-16 18:23:43 [INFO] - Transferring CatC_0000_2... 2024-09-16 18:23:44 [INFO] - Transferring CatC_0000_3... 2024-09-16 18:23:44 [INFO] - Transferring CatC_0000_4... 2024-09-16 18:23:44 [INFO] - Transferring CatD_0000_1... 2024-09-16 18:23:44 [INFO] - Transferring CatD_0000_2... 2024-09-16 18:23:44 [INFO] - Training LDA models for all matched features. 2024-09-16 18:23:44 [INFO] - #{+1} = 465, #{-1} = 31, #{+2} = 1109, #{-2} = 115 2024-09-16 18:23:44 [INFO] - Standardized coefficients: 2024-09-16 18:23:44 [INFO] - log10(intensity): 0.722371703990625 2024-09-16 18:23:44 [INFO] - log10(KL): -0.4489439386734887 2024-09-16 18:23:44 [INFO] - abs(ppm): -0.4911187351805933 2024-09-16 18:23:44 [INFO] - RT diff: -0.25793354560032056 2024-09-16 18:23:44 [INFO] - Fitting a mixture model... 2024-09-16 18:23:44 [INFO] - Matching-between-runs: CatB_0000_2... 2024-09-16 18:23:44 [INFO] - Calculating correlations between all other runs... 2024-09-16 18:23:44 [INFO] - Reading index from /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0000_2.quantindex 2024-09-16 18:23:44 [INFO] - Transferring CatA_0000_1... 2024-09-16 18:23:44 [INFO] - Transferring CatA_0000_4... 2024-09-16 18:23:44 [INFO] - Transferring CatB_0000_1... 2024-09-16 18:23:44 [INFO] - Transferring CatB_0000_3... 2024-09-16 18:23:44 [INFO] - Transferring CatB_0000_4... 2024-09-16 18:23:44 [INFO] - Transferring CatB_0015_1... 2024-09-16 18:23:44 [INFO] - Transferring CatB_0015_2... 2024-09-16 18:23:44 [INFO] - Transferring CatB_0015_3... 2024-09-16 18:23:44 [INFO] - Transferring CatB_0015_4... 2024-09-16 18:23:44 [INFO] - Transferring CatB_0060_1... 2024-09-16 18:23:44 [INFO] - Transferring CatB_0060_2... 2024-09-16 18:23:44 [INFO] - Transferring CatB_0060_4... 2024-09-16 18:23:44 [INFO] - Transferring CatC_0000_4... 2024-09-16 18:23:44 [INFO] - Transferring CatD_0000_1... 2024-09-16 18:23:44 [INFO] - Transferring CatD_0000_2... 2024-09-16 18:23:44 [INFO] - Training LDA models for all matched features. 2024-09-16 18:23:44 [INFO] - #{+1} = 514, #{-1} = 47, #{+2} = 1069, #{-2} = 107 2024-09-16 18:23:44 [INFO] - Standardized coefficients: 2024-09-16 18:23:44 [INFO] - log10(intensity): 0.8077587512648063 2024-09-16 18:23:44 [INFO] - log10(KL): -0.3625170512381213 2024-09-16 18:23:44 [INFO] - abs(ppm): -0.4612631577658624 2024-09-16 18:23:44 [INFO] - RT diff: -0.2754044238455424 2024-09-16 18:23:44 [INFO] - Fitting a mixture model... 2024-09-16 18:23:44 [INFO] - Matching-between-runs: CatB_0000_3... 2024-09-16 18:23:44 [INFO] - Calculating correlations between all other runs... 2024-09-16 18:23:44 [INFO] - Reading index from /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0000_3.quantindex 2024-09-16 18:23:44 [INFO] - Transferring CatB_0000_1... 2024-09-16 18:23:44 [INFO] - Transferring CatB_0000_2... 2024-09-16 18:23:44 [INFO] - Transferring CatB_0000_4... 2024-09-16 18:23:44 [INFO] - Transferring CatB_0015_1... 2024-09-16 18:23:44 [INFO] - Transferring CatB_0015_2... 2024-09-16 18:23:44 [INFO] - Transferring CatB_0015_3... 2024-09-16 18:23:44 [INFO] - Transferring CatB_0015_4... 2024-09-16 18:23:44 [INFO] - Transferring CatB_0060_1... 2024-09-16 18:23:44 [INFO] - Transferring CatB_0060_2... 2024-09-16 18:23:44 [INFO] - Transferring CatB_0060_4... 2024-09-16 18:23:44 [INFO] - Transferring CatC_0000_2... 2024-09-16 18:23:44 [INFO] - Transferring CatC_0000_3... 2024-09-16 18:23:44 [INFO] - Transferring CatC_0000_4... 2024-09-16 18:23:44 [INFO] - Transferring CatD_0000_1... 2024-09-16 18:23:44 [INFO] - Transferring CatD_0000_2... 2024-09-16 18:23:44 [INFO] - Training LDA models for all matched features. 2024-09-16 18:23:44 [INFO] - #{+1} = 467, #{-1} = 42, #{+2} = 1168, #{-2} = 115 2024-09-16 18:23:44 [INFO] - Standardized coefficients: 2024-09-16 18:23:44 [INFO] - log10(intensity): 0.8072186844918705 2024-09-16 18:23:44 [INFO] - log10(KL): -0.34923891336685964 2024-09-16 18:23:44 [INFO] - abs(ppm): -0.43385648854823733 2024-09-16 18:23:44 [INFO] - RT diff: -0.1954449389013231 2024-09-16 18:23:44 [INFO] - Fitting a mixture model... 2024-09-16 18:23:44 [INFO] - Matching-between-runs: CatB_0000_4... 2024-09-16 18:23:44 [INFO] - Calculating correlations between all other runs... 2024-09-16 18:23:44 [INFO] - Reading index from /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0000_4.quantindex 2024-09-16 18:23:45 [INFO] - Transferring CatB_0000_1... 2024-09-16 18:23:45 [INFO] - Transferring CatB_0000_2... 2024-09-16 18:23:45 [INFO] - Transferring CatB_0000_3... 2024-09-16 18:23:45 [INFO] - Transferring CatB_0015_1... 2024-09-16 18:23:45 [INFO] - Transferring CatB_0015_2... 2024-09-16 18:23:45 [INFO] - Transferring CatB_0015_3... 2024-09-16 18:23:45 [INFO] - Transferring CatB_0015_4... 2024-09-16 18:23:45 [INFO] - Transferring CatB_0060_1... 2024-09-16 18:23:45 [INFO] - Transferring CatB_0060_2... 2024-09-16 18:23:45 [INFO] - Transferring CatB_0060_4... 2024-09-16 18:23:45 [INFO] - Transferring CatC_0000_2... 2024-09-16 18:23:45 [INFO] - Transferring CatC_0000_3... 2024-09-16 18:23:45 [INFO] - Transferring CatC_0000_4... 2024-09-16 18:23:45 [INFO] - Transferring CatD_0000_1... 2024-09-16 18:23:45 [INFO] - Transferring CatD_0000_2... 2024-09-16 18:23:45 [INFO] - Training LDA models for all matched features. 2024-09-16 18:23:45 [INFO] - #{+1} = 457, #{-1} = 47, #{+2} = 1120, #{-2} = 126 2024-09-16 18:23:45 [INFO] - Standardized coefficients: 2024-09-16 18:23:45 [INFO] - log10(intensity): 0.7149009492111801 2024-09-16 18:23:45 [INFO] - log10(KL): -0.5355880477817252 2024-09-16 18:23:45 [INFO] - abs(ppm): -0.4368981770100857 2024-09-16 18:23:45 [INFO] - RT diff: -0.1837421655217777 2024-09-16 18:23:45 [INFO] - Fitting a mixture model... 2024-09-16 18:23:45 [INFO] - Matching-between-runs: CatB_0015_1... 2024-09-16 18:23:45 [INFO] - Calculating correlations between all other runs... 2024-09-16 18:23:45 [INFO] - Reading index from /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0015_1.quantindex 2024-09-16 18:23:45 [INFO] - Transferring CatB_0000_1... 2024-09-16 18:23:45 [INFO] - Transferring CatB_0000_2... 2024-09-16 18:23:45 [INFO] - Transferring CatB_0000_3... 2024-09-16 18:23:45 [INFO] - Transferring CatB_0000_4... 2024-09-16 18:23:45 [INFO] - Transferring CatB_0015_2... 2024-09-16 18:23:45 [INFO] - Transferring CatB_0015_3... 2024-09-16 18:23:45 [INFO] - Transferring CatB_0015_4... 2024-09-16 18:23:45 [INFO] - Transferring CatB_0060_1... 2024-09-16 18:23:45 [INFO] - Transferring CatB_0060_2... 2024-09-16 18:23:45 [INFO] - Transferring CatB_0060_3... 2024-09-16 18:23:45 [INFO] - Transferring CatB_0060_4... 2024-09-16 18:23:45 [INFO] - Transferring CatC_0000_2... 2024-09-16 18:23:45 [INFO] - Transferring CatC_0000_4... 2024-09-16 18:23:45 [INFO] - Transferring CatD_0000_1... 2024-09-16 18:23:45 [INFO] - Transferring CatD_0000_2... 2024-09-16 18:23:45 [INFO] - Training LDA models for all matched features. 2024-09-16 18:23:45 [INFO] - #{+1} = 503, #{-1} = 46, #{+2} = 1283, #{-2} = 121 2024-09-16 18:23:45 [INFO] - Standardized coefficients: 2024-09-16 18:23:45 [INFO] - log10(intensity): 0.8356551847230043 2024-09-16 18:23:45 [INFO] - log10(KL): -0.30109529793522966 2024-09-16 18:23:45 [INFO] - abs(ppm): -0.39061137593932543 2024-09-16 18:23:45 [INFO] - RT diff: -0.24175356624803732 2024-09-16 18:23:45 [INFO] - Fitting a mixture model... 2024-09-16 18:23:45 [INFO] - Matching-between-runs: CatB_0015_2... 2024-09-16 18:23:45 [INFO] - Calculating correlations between all other runs... 2024-09-16 18:23:45 [INFO] - Reading index from /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0015_2.quantindex 2024-09-16 18:23:45 [INFO] - Transferring CatA_0000_3... 2024-09-16 18:23:45 [INFO] - Transferring CatB_0000_1... 2024-09-16 18:23:45 [INFO] - Transferring CatB_0000_2... 2024-09-16 18:23:45 [INFO] - Transferring CatB_0000_3... 2024-09-16 18:23:45 [INFO] - Transferring CatB_0000_4... 2024-09-16 18:23:45 [INFO] - Transferring CatB_0015_1... 2024-09-16 18:23:45 [INFO] - Transferring CatB_0015_3... 2024-09-16 18:23:45 [INFO] - Transferring CatB_0015_4... 2024-09-16 18:23:45 [INFO] - Transferring CatB_0060_1... 2024-09-16 18:23:45 [INFO] - Transferring CatB_0060_2... 2024-09-16 18:23:46 [INFO] - Transferring CatB_0060_3... 2024-09-16 18:23:46 [INFO] - Transferring CatB_0060_4... 2024-09-16 18:23:46 [INFO] - Transferring CatC_0000_4... 2024-09-16 18:23:46 [INFO] - Transferring CatD_0000_1... 2024-09-16 18:23:46 [INFO] - Transferring CatD_0000_2... 2024-09-16 18:23:46 [INFO] - Training LDA models for all matched features. 2024-09-16 18:23:46 [INFO] - #{+1} = 478, #{-1} = 43, #{+2} = 1182, #{-2} = 115 2024-09-16 18:23:46 [INFO] - Standardized coefficients: 2024-09-16 18:23:46 [INFO] - log10(intensity): 0.6971742895366412 2024-09-16 18:23:46 [INFO] - log10(KL): -0.5441631723753436 2024-09-16 18:23:46 [INFO] - abs(ppm): -0.4745719506721997 2024-09-16 18:23:46 [INFO] - RT diff: -0.13495242799768511 2024-09-16 18:23:46 [INFO] - Fitting a mixture model... 2024-09-16 18:23:46 [INFO] - Matching-between-runs: CatB_0015_3... 2024-09-16 18:23:46 [INFO] - Calculating correlations between all other runs... 2024-09-16 18:23:46 [INFO] - Reading index from /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0015_3.quantindex 2024-09-16 18:23:46 [INFO] - Transferring CatB_0000_1... 2024-09-16 18:23:46 [INFO] - Transferring CatB_0000_2... 2024-09-16 18:23:46 [INFO] - Transferring CatB_0000_3... 2024-09-16 18:23:46 [INFO] - Transferring CatB_0000_4... 2024-09-16 18:23:46 [INFO] - Transferring CatB_0015_1... 2024-09-16 18:23:46 [INFO] - Transferring CatB_0015_2... 2024-09-16 18:23:46 [INFO] - Transferring CatB_0015_4... 2024-09-16 18:23:46 [INFO] - Transferring CatB_0060_1... 2024-09-16 18:23:46 [INFO] - Transferring CatB_0060_2... 2024-09-16 18:23:46 [INFO] - Transferring CatB_0060_3... 2024-09-16 18:23:46 [INFO] - Transferring CatB_0060_4... 2024-09-16 18:23:46 [INFO] - Transferring CatC_0000_2... 2024-09-16 18:23:46 [INFO] - Transferring CatC_0000_4... 2024-09-16 18:23:46 [INFO] - Transferring CatD_0000_1... 2024-09-16 18:23:46 [INFO] - Transferring CatD_0000_2... 2024-09-16 18:23:46 [INFO] - Training LDA models for all matched features. 2024-09-16 18:23:46 [INFO] - #{+1} = 488, #{-1} = 46, #{+2} = 1262, #{-2} = 114 2024-09-16 18:23:46 [INFO] - Standardized coefficients: 2024-09-16 18:23:46 [INFO] - log10(intensity): 0.829029582650304 2024-09-16 18:23:46 [INFO] - log10(KL): -0.3117728699048592 2024-09-16 18:23:46 [INFO] - abs(ppm): -0.4192106610083747 2024-09-16 18:23:46 [INFO] - RT diff: -0.19942429736336534 2024-09-16 18:23:46 [INFO] - Fitting a mixture model... 2024-09-16 18:23:46 [INFO] - Matching-between-runs: CatB_0015_4... 2024-09-16 18:23:46 [INFO] - Calculating correlations between all other runs... 2024-09-16 18:23:46 [INFO] - Reading index from /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0015_4.quantindex 2024-09-16 18:23:46 [INFO] - Transferring CatB_0000_1... 2024-09-16 18:23:46 [INFO] - Transferring CatB_0000_2... 2024-09-16 18:23:46 [INFO] - Transferring CatB_0000_3... 2024-09-16 18:23:46 [INFO] - Transferring CatB_0000_4... 2024-09-16 18:23:46 [INFO] - Transferring CatB_0015_1... 2024-09-16 18:23:46 [INFO] - Transferring CatB_0015_2... 2024-09-16 18:23:46 [INFO] - Transferring CatB_0015_3... 2024-09-16 18:23:46 [INFO] - Transferring CatB_0060_1... 2024-09-16 18:23:46 [INFO] - Transferring CatB_0060_2... 2024-09-16 18:23:46 [INFO] - Transferring CatB_0060_3... 2024-09-16 18:23:46 [INFO] - Transferring CatB_0060_4... 2024-09-16 18:23:46 [INFO] - Transferring CatC_0000_3... 2024-09-16 18:23:46 [INFO] - Transferring CatC_0000_4... 2024-09-16 18:23:46 [INFO] - Transferring CatD_0000_1... 2024-09-16 18:23:46 [INFO] - Transferring CatD_0000_2... 2024-09-16 18:23:46 [INFO] - Training LDA models for all matched features. 2024-09-16 18:23:46 [INFO] - #{+1} = 477, #{-1} = 45, #{+2} = 1283, #{-2} = 111 2024-09-16 18:23:46 [INFO] - Standardized coefficients: 2024-09-16 18:23:46 [INFO] - log10(intensity): 0.8021236081105083 2024-09-16 18:23:46 [INFO] - log10(KL): -0.32710158560213176 2024-09-16 18:23:46 [INFO] - abs(ppm): -0.5179554512958195 2024-09-16 18:23:46 [INFO] - RT diff: -0.19504849071411212 2024-09-16 18:23:46 [INFO] - Fitting a mixture model... 2024-09-16 18:23:46 [INFO] - Matching-between-runs: CatB_0060_1... 2024-09-16 18:23:46 [INFO] - Calculating correlations between all other runs... 2024-09-16 18:23:46 [INFO] - Reading index from /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0060_1.quantindex 2024-09-16 18:23:47 [INFO] - Transferring CatB_0000_1... 2024-09-16 18:23:47 [INFO] - Transferring CatB_0000_2... 2024-09-16 18:23:47 [INFO] - Transferring CatB_0000_3... 2024-09-16 18:23:47 [INFO] - Transferring CatB_0000_4... 2024-09-16 18:23:47 [INFO] - Transferring CatB_0015_1... 2024-09-16 18:23:47 [INFO] - Transferring CatB_0015_2... 2024-09-16 18:23:47 [INFO] - Transferring CatB_0015_3... 2024-09-16 18:23:47 [INFO] - Transferring CatB_0015_4... 2024-09-16 18:23:47 [INFO] - Transferring CatB_0060_2... 2024-09-16 18:23:47 [INFO] - Transferring CatB_0060_3... 2024-09-16 18:23:47 [INFO] - Transferring CatB_0060_4... 2024-09-16 18:23:47 [INFO] - Transferring CatC_0000_3... 2024-09-16 18:23:47 [INFO] - Transferring CatC_0000_4... 2024-09-16 18:23:47 [INFO] - Transferring CatD_0000_1... 2024-09-16 18:23:47 [INFO] - Transferring CatD_0000_2... 2024-09-16 18:23:47 [INFO] - Training LDA models for all matched features. 2024-09-16 18:23:47 [INFO] - #{+1} = 452, #{-1} = 48, #{+2} = 1328, #{-2} = 122 2024-09-16 18:23:47 [INFO] - Standardized coefficients: 2024-09-16 18:23:47 [INFO] - log10(intensity): 0.7155658937414359 2024-09-16 18:23:47 [INFO] - log10(KL): -0.4723863472500445 2024-09-16 18:23:47 [INFO] - abs(ppm): -0.4974646326291921 2024-09-16 18:23:47 [INFO] - RT diff: -0.22358952771805157 2024-09-16 18:23:47 [INFO] - Fitting a mixture model... 2024-09-16 18:23:47 [INFO] - Matching-between-runs: CatB_0060_2... 2024-09-16 18:23:47 [INFO] - Calculating correlations between all other runs... 2024-09-16 18:23:47 [INFO] - Reading index from /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0060_2.quantindex 2024-09-16 18:23:47 [INFO] - Transferring CatB_0000_1... 2024-09-16 18:23:47 [INFO] - Transferring CatB_0000_2... 2024-09-16 18:23:47 [INFO] - Transferring CatB_0000_3... 2024-09-16 18:23:47 [INFO] - Transferring CatB_0000_4... 2024-09-16 18:23:47 [INFO] - Transferring CatB_0015_1... 2024-09-16 18:23:47 [INFO] - Transferring CatB_0015_2... 2024-09-16 18:23:47 [INFO] - Transferring CatB_0015_3... 2024-09-16 18:23:47 [INFO] - Transferring CatB_0015_4... 2024-09-16 18:23:47 [INFO] - Transferring CatB_0060_1... 2024-09-16 18:23:47 [INFO] - Transferring CatB_0060_3... 2024-09-16 18:23:47 [INFO] - Transferring CatB_0060_4... 2024-09-16 18:23:47 [INFO] - Transferring CatC_0000_2... 2024-09-16 18:23:47 [INFO] - Transferring CatC_0000_4... 2024-09-16 18:23:47 [INFO] - Transferring CatD_0000_1... 2024-09-16 18:23:47 [INFO] - Transferring CatD_0000_2... 2024-09-16 18:23:47 [INFO] - Training LDA models for all matched features. 2024-09-16 18:23:47 [INFO] - #{+1} = 449, #{-1} = 57, #{+2} = 1330, #{-2} = 119 2024-09-16 18:23:47 [INFO] - Standardized coefficients: 2024-09-16 18:23:47 [INFO] - log10(intensity): 0.6462424431819063 2024-09-16 18:23:47 [INFO] - log10(KL): -0.5393013739613843 2024-09-16 18:23:47 [INFO] - abs(ppm): -0.4957690539217645 2024-09-16 18:23:47 [INFO] - RT diff: -0.24288322034637805 2024-09-16 18:23:47 [INFO] - Fitting a mixture model... 2024-09-16 18:23:47 [INFO] - Matching-between-runs: CatB_0060_3... 2024-09-16 18:23:47 [INFO] - Calculating correlations between all other runs... 2024-09-16 18:23:47 [INFO] - Reading index from /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0060_3.quantindex 2024-09-16 18:23:47 [INFO] - Transferring CatB_0000_1... 2024-09-16 18:23:47 [INFO] - Transferring CatB_0000_2... 2024-09-16 18:23:47 [INFO] - Transferring CatB_0000_3... 2024-09-16 18:23:47 [INFO] - Transferring CatB_0000_4... 2024-09-16 18:23:47 [INFO] - Transferring CatB_0015_1... 2024-09-16 18:23:47 [INFO] - Transferring CatB_0015_2... 2024-09-16 18:23:47 [INFO] - Transferring CatB_0015_3... 2024-09-16 18:23:47 [INFO] - Transferring CatB_0015_4... 2024-09-16 18:23:47 [INFO] - Transferring CatB_0060_1... 2024-09-16 18:23:47 [INFO] - Transferring CatB_0060_2... 2024-09-16 18:23:47 [INFO] - Transferring CatB_0060_4... 2024-09-16 18:23:47 [INFO] - Transferring CatC_0000_3... 2024-09-16 18:23:47 [INFO] - Transferring CatC_0000_4... 2024-09-16 18:23:47 [INFO] - Transferring CatD_0000_1... 2024-09-16 18:23:47 [INFO] - Transferring CatD_0000_2... 2024-09-16 18:23:48 [INFO] - Training LDA models for all matched features. 2024-09-16 18:23:48 [INFO] - #{+1} = 432, #{-1} = 40, #{+2} = 1335, #{-2} = 113 2024-09-16 18:23:48 [INFO] - Standardized coefficients: 2024-09-16 18:23:48 [INFO] - log10(intensity): 0.7960942689956911 2024-09-16 18:23:48 [INFO] - log10(KL): -0.34073000406009957 2024-09-16 18:23:48 [INFO] - abs(ppm): -0.4011657793749551 2024-09-16 18:23:48 [INFO] - RT diff: -0.2986687072056687 2024-09-16 18:23:48 [INFO] - Fitting a mixture model... 2024-09-16 18:23:48 [INFO] - Matching-between-runs: CatB_0060_4... 2024-09-16 18:23:48 [INFO] - Calculating correlations between all other runs... 2024-09-16 18:23:48 [INFO] - Reading index from /home/nanopore-catalyst/HDD/mspms/raw_data/CatB_0060_4.quantindex 2024-09-16 18:23:48 [INFO] - Transferring CatB_0000_1... 2024-09-16 18:23:48 [INFO] - Transferring CatB_0000_2... 2024-09-16 18:23:48 [INFO] - Transferring CatB_0000_3... 2024-09-16 18:23:48 [INFO] - Transferring CatB_0000_4... 2024-09-16 18:23:48 [INFO] - Transferring CatB_0015_1... 2024-09-16 18:23:48 [INFO] - Transferring CatB_0015_2... 2024-09-16 18:23:48 [INFO] - Transferring CatB_0015_3... 2024-09-16 18:23:48 [INFO] - Transferring CatB_0015_4... 2024-09-16 18:23:48 [INFO] - Transferring CatB_0060_1... 2024-09-16 18:23:48 [INFO] - Transferring CatB_0060_2... 2024-09-16 18:23:48 [INFO] - Transferring CatB_0060_3... 2024-09-16 18:23:48 [INFO] - Transferring CatC_0000_3... 2024-09-16 18:23:48 [INFO] - Transferring CatC_0000_4... 2024-09-16 18:23:48 [INFO] - Transferring CatD_0000_1... 2024-09-16 18:23:48 [INFO] - Transferring CatD_0000_2... 2024-09-16 18:23:48 [INFO] - Training LDA models for all matched features. 2024-09-16 18:23:48 [INFO] - #{+1} = 444, #{-1} = 41, #{+2} = 1358, #{-2} = 125 2024-09-16 18:23:48 [INFO] - Standardized coefficients: 2024-09-16 18:23:48 [INFO] - log10(intensity): 0.8069258014616706 2024-09-16 18:23:48 [INFO] - log10(KL): -0.31604704044002113 2024-09-16 18:23:48 [INFO] - abs(ppm): -0.4934273081184205 2024-09-16 18:23:48 [INFO] - RT diff: -0.292965655239775 2024-09-16 18:23:48 [INFO] - Fitting a mixture model... 2024-09-16 18:23:48 [INFO] - Matching-between-runs: CatC_0000_1... 2024-09-16 18:23:48 [INFO] - Calculating correlations between all other runs... 2024-09-16 18:23:48 [INFO] - Reading index from /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0000_1.quantindex 2024-09-16 18:23:48 [INFO] - Transferring CatA_0000_1... 2024-09-16 18:23:48 [INFO] - Transferring CatA_0000_2... 2024-09-16 18:23:48 [INFO] - Transferring CatA_0000_3... 2024-09-16 18:23:48 [INFO] - Transferring CatA_0000_4... 2024-09-16 18:23:48 [INFO] - Transferring CatC_0000_2... 2024-09-16 18:23:48 [INFO] - Transferring CatC_0000_3... 2024-09-16 18:23:48 [INFO] - Transferring CatC_0000_4... 2024-09-16 18:23:48 [INFO] - Transferring CatC_0030_1... 2024-09-16 18:23:48 [INFO] - Transferring CatC_0030_2... 2024-09-16 18:23:48 [INFO] - Transferring CatC_0030_3... 2024-09-16 18:23:48 [INFO] - Transferring CatC_0030_4... 2024-09-16 18:23:48 [INFO] - Transferring CatC_0090_1... 2024-09-16 18:23:48 [INFO] - Transferring CatC_0090_2... 2024-09-16 18:23:48 [INFO] - Transferring CatC_0090_3... 2024-09-16 18:23:48 [INFO] - Transferring CatC_0090_4... 2024-09-16 18:23:48 [INFO] - Training LDA models for all matched features. 2024-09-16 18:23:48 [INFO] - #{+1} = 336, #{-1} = 27, #{+2} = 1085, #{-2} = 88 2024-09-16 18:23:48 [INFO] - Standardized coefficients: 2024-09-16 18:23:48 [INFO] - log10(intensity): 0.7244394271334975 2024-09-16 18:23:48 [INFO] - log10(KL): -0.3996950071515193 2024-09-16 18:23:48 [INFO] - abs(ppm): -0.438516741347984 2024-09-16 18:23:48 [INFO] - RT diff: -0.43156160441752006 2024-09-16 18:23:48 [INFO] - Fitting a mixture model... 2024-09-16 18:23:48 [INFO] - Matching-between-runs: CatC_0000_2... 2024-09-16 18:23:48 [INFO] - Calculating correlations between all other runs... 2024-09-16 18:23:48 [INFO] - Reading index from /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0000_2.quantindex 2024-09-16 18:23:48 [INFO] - Transferring CatA_0000_1... 2024-09-16 18:23:48 [INFO] - Transferring CatA_0000_2... 2024-09-16 18:23:48 [INFO] - Transferring CatA_0000_3... 2024-09-16 18:23:48 [INFO] - Transferring CatA_0000_4... 2024-09-16 18:23:48 [INFO] - Transferring CatC_0000_1... 2024-09-16 18:23:48 [INFO] - Transferring CatC_0000_3... 2024-09-16 18:23:48 [INFO] - Transferring CatC_0000_4... 2024-09-16 18:23:49 [INFO] - Transferring CatC_0030_1... 2024-09-16 18:23:49 [INFO] - Transferring CatC_0030_2... 2024-09-16 18:23:49 [INFO] - Transferring CatC_0030_3... 2024-09-16 18:23:49 [INFO] - Transferring CatC_0030_4... 2024-09-16 18:23:49 [INFO] - Transferring CatC_0090_1... 2024-09-16 18:23:49 [INFO] - Transferring CatC_0090_2... 2024-09-16 18:23:49 [INFO] - Transferring CatC_0090_3... 2024-09-16 18:23:49 [INFO] - Transferring CatC_0090_4... 2024-09-16 18:23:49 [INFO] - Training LDA models for all matched features. 2024-09-16 18:23:49 [INFO] - #{+1} = 363, #{-1} = 35, #{+2} = 1062, #{-2} = 91 2024-09-16 18:23:49 [INFO] - Standardized coefficients: 2024-09-16 18:23:49 [INFO] - log10(intensity): 0.8008251900597745 2024-09-16 18:23:49 [INFO] - log10(KL): -0.3074061125370793 2024-09-16 18:23:49 [INFO] - abs(ppm): -0.4128408007713132 2024-09-16 18:23:49 [INFO] - RT diff: -0.43341648390806475 2024-09-16 18:23:49 [INFO] - Fitting a mixture model... 2024-09-16 18:23:49 [INFO] - Matching-between-runs: CatC_0000_3... 2024-09-16 18:23:49 [INFO] - Calculating correlations between all other runs... 2024-09-16 18:23:49 [INFO] - Reading index from /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0000_3.quantindex 2024-09-16 18:23:49 [INFO] - Transferring CatA_0000_1... 2024-09-16 18:23:49 [INFO] - Transferring CatA_0000_2... 2024-09-16 18:23:49 [INFO] - Transferring CatA_0000_3... 2024-09-16 18:23:49 [INFO] - Transferring CatA_0000_4... 2024-09-16 18:23:49 [INFO] - Transferring CatC_0000_1... 2024-09-16 18:23:49 [INFO] - Transferring CatC_0000_2... 2024-09-16 18:23:49 [INFO] - Transferring CatC_0000_4... 2024-09-16 18:23:49 [INFO] - Transferring CatC_0030_1... 2024-09-16 18:23:49 [INFO] - Transferring CatC_0030_2... 2024-09-16 18:23:49 [INFO] - Transferring CatC_0030_3... 2024-09-16 18:23:49 [INFO] - Transferring CatC_0030_4... 2024-09-16 18:23:49 [INFO] - Transferring CatC_0090_1... 2024-09-16 18:23:49 [INFO] - Transferring CatC_0090_2... 2024-09-16 18:23:49 [INFO] - Transferring CatC_0090_3... 2024-09-16 18:23:49 [INFO] - Transferring CatC_0090_4... 2024-09-16 18:23:49 [INFO] - Training LDA models for all matched features. 2024-09-16 18:23:49 [INFO] - #{+1} = 364, #{-1} = 36, #{+2} = 1060, #{-2} = 85 2024-09-16 18:23:49 [INFO] - Standardized coefficients: 2024-09-16 18:23:49 [INFO] - log10(intensity): 0.5893044534978089 2024-09-16 18:23:49 [INFO] - log10(KL): -0.46042745982333544 2024-09-16 18:23:49 [INFO] - abs(ppm): -0.4536065453893718 2024-09-16 18:23:49 [INFO] - RT diff: -0.49478517591654436 2024-09-16 18:23:49 [INFO] - Fitting a mixture model... 2024-09-16 18:23:49 [INFO] - Matching-between-runs: CatC_0000_4... 2024-09-16 18:23:49 [INFO] - Calculating correlations between all other runs... 2024-09-16 18:23:49 [INFO] - Reading index from /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0000_4.quantindex 2024-09-16 18:23:49 [INFO] - Transferring CatA_0000_1... 2024-09-16 18:23:49 [INFO] - Transferring CatA_0000_2... 2024-09-16 18:23:49 [INFO] - Transferring CatA_0000_3... 2024-09-16 18:23:49 [INFO] - Transferring CatA_0000_4... 2024-09-16 18:23:49 [INFO] - Transferring CatC_0000_1... 2024-09-16 18:23:49 [INFO] - Transferring CatC_0000_2... 2024-09-16 18:23:49 [INFO] - Transferring CatC_0000_3... 2024-09-16 18:23:49 [INFO] - Transferring CatC_0030_1... 2024-09-16 18:23:49 [INFO] - Transferring CatC_0030_2... 2024-09-16 18:23:49 [INFO] - Transferring CatC_0030_3... 2024-09-16 18:23:49 [INFO] - Transferring CatC_0030_4... 2024-09-16 18:23:49 [INFO] - Transferring CatC_0090_1... 2024-09-16 18:23:49 [INFO] - Transferring CatC_0090_2... 2024-09-16 18:23:49 [INFO] - Transferring CatC_0090_3... 2024-09-16 18:23:49 [INFO] - Transferring CatC_0090_4... 2024-09-16 18:23:49 [INFO] - Training LDA models for all matched features. 2024-09-16 18:23:49 [INFO] - #{+1} = 328, #{-1} = 25, #{+2} = 1085, #{-2} = 92 2024-09-16 18:23:49 [INFO] - Standardized coefficients: 2024-09-16 18:23:49 [INFO] - log10(intensity): 0.6882375299341982 2024-09-16 18:23:49 [INFO] - log10(KL): -0.3393732595633895 2024-09-16 18:23:49 [INFO] - abs(ppm): -0.5131572050254253 2024-09-16 18:23:49 [INFO] - RT diff: -0.4413569950122703 2024-09-16 18:23:49 [INFO] - Fitting a mixture model... 2024-09-16 18:23:49 [INFO] - Matching-between-runs: CatC_0030_1... 2024-09-16 18:23:49 [INFO] - Calculating correlations between all other runs... 2024-09-16 18:23:50 [INFO] - Reading index from /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0030_1.quantindex 2024-09-16 18:23:50 [INFO] - Transferring CatA_0000_1... 2024-09-16 18:23:50 [INFO] - Transferring CatA_0000_2... 2024-09-16 18:23:50 [INFO] - Transferring CatA_0000_3... 2024-09-16 18:23:50 [INFO] - Transferring CatA_0000_4... 2024-09-16 18:23:50 [INFO] - Transferring CatC_0000_1... 2024-09-16 18:23:50 [INFO] - Transferring CatC_0000_2... 2024-09-16 18:23:50 [INFO] - Transferring CatC_0000_3... 2024-09-16 18:23:50 [INFO] - Transferring CatC_0000_4... 2024-09-16 18:23:50 [INFO] - Transferring CatC_0030_2... 2024-09-16 18:23:50 [INFO] - Transferring CatC_0030_3... 2024-09-16 18:23:50 [INFO] - Transferring CatC_0030_4... 2024-09-16 18:23:50 [INFO] - Transferring CatC_0090_1... 2024-09-16 18:23:50 [INFO] - Transferring CatC_0090_2... 2024-09-16 18:23:50 [INFO] - Transferring CatC_0090_3... 2024-09-16 18:23:50 [INFO] - Transferring CatC_0090_4... 2024-09-16 18:23:50 [INFO] - Training LDA models for all matched features. 2024-09-16 18:23:50 [INFO] - #{+1} = 344, #{-1} = 28, #{+2} = 1143, #{-2} = 108 2024-09-16 18:23:50 [INFO] - Standardized coefficients: 2024-09-16 18:23:50 [INFO] - log10(intensity): 0.6600002028375114 2024-09-16 18:23:50 [INFO] - log10(KL): -0.47683794479553326 2024-09-16 18:23:50 [INFO] - abs(ppm): -0.4323113505430722 2024-09-16 18:23:50 [INFO] - RT diff: -0.4405565254727982 2024-09-16 18:23:50 [INFO] - Fitting a mixture model... 2024-09-16 18:23:50 [INFO] - Matching-between-runs: CatC_0030_2... 2024-09-16 18:23:50 [INFO] - Calculating correlations between all other runs... 2024-09-16 18:23:50 [INFO] - Reading index from /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0030_2.quantindex 2024-09-16 18:23:50 [INFO] - Transferring CatA_0000_1... 2024-09-16 18:23:50 [INFO] - Transferring CatA_0000_2... 2024-09-16 18:23:50 [INFO] - Transferring CatA_0000_3... 2024-09-16 18:23:50 [INFO] - Transferring CatA_0000_4... 2024-09-16 18:23:50 [INFO] - Transferring CatC_0000_1... 2024-09-16 18:23:50 [INFO] - Transferring CatC_0000_2... 2024-09-16 18:23:50 [INFO] - Transferring CatC_0000_3... 2024-09-16 18:23:50 [INFO] - Transferring CatC_0000_4... 2024-09-16 18:23:50 [INFO] - Transferring CatC_0030_1... 2024-09-16 18:23:50 [INFO] - Transferring CatC_0030_3... 2024-09-16 18:23:50 [INFO] - Transferring CatC_0030_4... 2024-09-16 18:23:50 [INFO] - Transferring CatC_0090_1... 2024-09-16 18:23:50 [INFO] - Transferring CatC_0090_2... 2024-09-16 18:23:50 [INFO] - Transferring CatC_0090_3... 2024-09-16 18:23:50 [INFO] - Transferring CatC_0090_4... 2024-09-16 18:23:50 [INFO] - Training LDA models for all matched features. 2024-09-16 18:23:50 [INFO] - #{+1} = 353, #{-1} = 26, #{+2} = 1143, #{-2} = 93 2024-09-16 18:23:50 [INFO] - Standardized coefficients: 2024-09-16 18:23:50 [INFO] - log10(intensity): 0.5852736025017524 2024-09-16 18:23:50 [INFO] - log10(KL): -0.40910656259531303 2024-09-16 18:23:50 [INFO] - abs(ppm): -0.5195520766518053 2024-09-16 18:23:50 [INFO] - RT diff: -0.48956044836820556 2024-09-16 18:23:50 [INFO] - Fitting a mixture model... 2024-09-16 18:23:50 [INFO] - Matching-between-runs: CatC_0030_3... 2024-09-16 18:23:50 [INFO] - Calculating correlations between all other runs... 2024-09-16 18:23:50 [INFO] - Reading index from /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0030_3.quantindex 2024-09-16 18:23:50 [INFO] - Transferring CatA_0000_1... 2024-09-16 18:23:50 [INFO] - Transferring CatA_0000_2... 2024-09-16 18:23:50 [INFO] - Transferring CatA_0000_3... 2024-09-16 18:23:50 [INFO] - Transferring CatA_0000_4... 2024-09-16 18:23:50 [INFO] - Transferring CatC_0000_1... 2024-09-16 18:23:50 [INFO] - Transferring CatC_0000_2... 2024-09-16 18:23:50 [INFO] - Transferring CatC_0000_3... 2024-09-16 18:23:50 [INFO] - Transferring CatC_0000_4... 2024-09-16 18:23:50 [INFO] - Transferring CatC_0030_1... 2024-09-16 18:23:50 [INFO] - Transferring CatC_0030_2... 2024-09-16 18:23:50 [INFO] - Transferring CatC_0030_4... 2024-09-16 18:23:50 [INFO] - Transferring CatC_0090_1... 2024-09-16 18:23:50 [INFO] - Transferring CatC_0090_2... 2024-09-16 18:23:50 [INFO] - Transferring CatC_0090_3... 2024-09-16 18:23:50 [INFO] - Transferring CatC_0090_4... 2024-09-16 18:23:51 [INFO] - Training LDA models for all matched features. 2024-09-16 18:23:51 [INFO] - #{+1} = 341, #{-1} = 28, #{+2} = 1143, #{-2} = 102 2024-09-16 18:23:51 [INFO] - Standardized coefficients: 2024-09-16 18:23:51 [INFO] - log10(intensity): 0.6807297444892848 2024-09-16 18:23:51 [INFO] - log10(KL): -0.3515992922918179 2024-09-16 18:23:51 [INFO] - abs(ppm): -0.4942059753910244 2024-09-16 18:23:51 [INFO] - RT diff: -0.46661051275195053 2024-09-16 18:23:51 [INFO] - Fitting a mixture model... 2024-09-16 18:23:51 [INFO] - Matching-between-runs: CatC_0030_4... 2024-09-16 18:23:51 [INFO] - Calculating correlations between all other runs... 2024-09-16 18:23:51 [INFO] - Reading index from /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0030_4.quantindex 2024-09-16 18:23:51 [INFO] - Transferring CatA_0000_1... 2024-09-16 18:23:51 [INFO] - Transferring CatA_0000_2... 2024-09-16 18:23:51 [INFO] - Transferring CatA_0000_3... 2024-09-16 18:23:51 [INFO] - Transferring CatA_0000_4... 2024-09-16 18:23:51 [INFO] - Transferring CatC_0000_1... 2024-09-16 18:23:51 [INFO] - Transferring CatC_0000_2... 2024-09-16 18:23:51 [INFO] - Transferring CatC_0000_3... 2024-09-16 18:23:51 [INFO] - Transferring CatC_0000_4... 2024-09-16 18:23:51 [INFO] - Transferring CatC_0030_1... 2024-09-16 18:23:51 [INFO] - Transferring CatC_0030_2... 2024-09-16 18:23:51 [INFO] - Transferring CatC_0030_3... 2024-09-16 18:23:51 [INFO] - Transferring CatC_0090_1... 2024-09-16 18:23:51 [INFO] - Transferring CatC_0090_2... 2024-09-16 18:23:51 [INFO] - Transferring CatC_0090_3... 2024-09-16 18:23:51 [INFO] - Transferring CatC_0090_4... 2024-09-16 18:23:51 [INFO] - Training LDA models for all matched features. 2024-09-16 18:23:51 [INFO] - #{+1} = 351, #{-1} = 37, #{+2} = 1123, #{-2} = 110 2024-09-16 18:23:51 [INFO] - Standardized coefficients: 2024-09-16 18:23:51 [INFO] - log10(intensity): 0.6556018658128493 2024-09-16 18:23:51 [INFO] - log10(KL): -0.487357316535261 2024-09-16 18:23:51 [INFO] - abs(ppm): -0.4195704763447294 2024-09-16 18:23:51 [INFO] - RT diff: -0.43970555816077 2024-09-16 18:23:51 [INFO] - Fitting a mixture model... 2024-09-16 18:23:51 [INFO] - Matching-between-runs: CatC_0090_1... 2024-09-16 18:23:51 [INFO] - Calculating correlations between all other runs... 2024-09-16 18:23:51 [INFO] - Reading index from /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0090_1.quantindex 2024-09-16 18:23:51 [INFO] - Transferring CatA_0000_1... 2024-09-16 18:23:51 [INFO] - Transferring CatA_0000_2... 2024-09-16 18:23:51 [INFO] - Transferring CatA_0000_3... 2024-09-16 18:23:51 [INFO] - Transferring CatA_0000_4... 2024-09-16 18:23:51 [INFO] - Transferring CatC_0000_1... 2024-09-16 18:23:51 [INFO] - Transferring CatC_0000_2... 2024-09-16 18:23:51 [INFO] - Transferring CatC_0000_3... 2024-09-16 18:23:51 [INFO] - Transferring CatC_0000_4... 2024-09-16 18:23:51 [INFO] - Transferring CatC_0030_1... 2024-09-16 18:23:51 [INFO] - Transferring CatC_0030_2... 2024-09-16 18:23:51 [INFO] - Transferring CatC_0030_3... 2024-09-16 18:23:51 [INFO] - Transferring CatC_0030_4... 2024-09-16 18:23:51 [INFO] - Transferring CatC_0090_2... 2024-09-16 18:23:51 [INFO] - Transferring CatC_0090_3... 2024-09-16 18:23:51 [INFO] - Transferring CatC_0090_4... 2024-09-16 18:23:51 [INFO] - Training LDA models for all matched features. 2024-09-16 18:23:51 [INFO] - #{+1} = 308, #{-1} = 32, #{+2} = 1211, #{-2} = 106 2024-09-16 18:23:51 [INFO] - Standardized coefficients: 2024-09-16 18:23:51 [INFO] - log10(intensity): 0.7330663975128955 2024-09-16 18:23:51 [INFO] - log10(KL): -0.33816534173662577 2024-09-16 18:23:51 [INFO] - abs(ppm): -0.48301362642551976 2024-09-16 18:23:51 [INFO] - RT diff: -0.42882117141727877 2024-09-16 18:23:51 [INFO] - Fitting a mixture model... 2024-09-16 18:23:51 [INFO] - Matching-between-runs: CatC_0090_2... 2024-09-16 18:23:51 [INFO] - Calculating correlations between all other runs... 2024-09-16 18:23:51 [INFO] - Reading index from /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0090_2.quantindex 2024-09-16 18:23:51 [INFO] - Transferring CatA_0000_1... 2024-09-16 18:23:51 [INFO] - Transferring CatA_0000_2... 2024-09-16 18:23:51 [INFO] - Transferring CatA_0000_3... 2024-09-16 18:23:51 [INFO] - Transferring CatA_0000_4... 2024-09-16 18:23:51 [INFO] - Transferring CatC_0000_1... 2024-09-16 18:23:51 [INFO] - Transferring CatC_0000_2... 2024-09-16 18:23:51 [INFO] - Transferring CatC_0000_3... 2024-09-16 18:23:51 [INFO] - Transferring CatC_0000_4... 2024-09-16 18:23:52 [INFO] - Transferring CatC_0030_1... 2024-09-16 18:23:52 [INFO] - Transferring CatC_0030_2... 2024-09-16 18:23:52 [INFO] - Transferring CatC_0030_3... 2024-09-16 18:23:52 [INFO] - Transferring CatC_0030_4... 2024-09-16 18:23:52 [INFO] - Transferring CatC_0090_1... 2024-09-16 18:23:52 [INFO] - Transferring CatC_0090_3... 2024-09-16 18:23:52 [INFO] - Transferring CatC_0090_4... 2024-09-16 18:23:52 [INFO] - Training LDA models for all matched features. 2024-09-16 18:23:52 [INFO] - #{+1} = 320, #{-1} = 34, #{+2} = 1203, #{-2} = 103 2024-09-16 18:23:52 [INFO] - Standardized coefficients: 2024-09-16 18:23:52 [INFO] - log10(intensity): 0.7313651497571557 2024-09-16 18:23:52 [INFO] - log10(KL): -0.3174204778406074 2024-09-16 18:23:52 [INFO] - abs(ppm): -0.473079323999408 2024-09-16 18:23:52 [INFO] - RT diff: -0.4669212731929712 2024-09-16 18:23:52 [INFO] - Fitting a mixture model... 2024-09-16 18:23:52 [INFO] - Matching-between-runs: CatC_0090_3... 2024-09-16 18:23:52 [INFO] - Calculating correlations between all other runs... 2024-09-16 18:23:52 [INFO] - Reading index from /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0090_3.quantindex 2024-09-16 18:23:52 [INFO] - Transferring CatA_0000_1... 2024-09-16 18:23:52 [INFO] - Transferring CatA_0000_2... 2024-09-16 18:23:52 [INFO] - Transferring CatA_0000_3... 2024-09-16 18:23:52 [INFO] - Transferring CatA_0000_4... 2024-09-16 18:23:52 [INFO] - Transferring CatC_0000_1... 2024-09-16 18:23:52 [INFO] - Transferring CatC_0000_2... 2024-09-16 18:23:52 [INFO] - Transferring CatC_0000_3... 2024-09-16 18:23:52 [INFO] - Transferring CatC_0000_4... 2024-09-16 18:23:52 [INFO] - Transferring CatC_0030_1... 2024-09-16 18:23:52 [INFO] - Transferring CatC_0030_2... 2024-09-16 18:23:52 [INFO] - Transferring CatC_0030_3... 2024-09-16 18:23:52 [INFO] - Transferring CatC_0030_4... 2024-09-16 18:23:52 [INFO] - Transferring CatC_0090_1... 2024-09-16 18:23:52 [INFO] - Transferring CatC_0090_2... 2024-09-16 18:23:52 [INFO] - Transferring CatC_0090_4... 2024-09-16 18:23:52 [INFO] - Training LDA models for all matched features. 2024-09-16 18:23:52 [INFO] - #{+1} = 310, #{-1} = 26, #{+2} = 1203, #{-2} = 106 2024-09-16 18:23:52 [INFO] - Standardized coefficients: 2024-09-16 18:23:52 [INFO] - log10(intensity): 0.5150897984261016 2024-09-16 18:23:52 [INFO] - log10(KL): -0.5485328978615168 2024-09-16 18:23:52 [INFO] - abs(ppm): -0.5023038685497231 2024-09-16 18:23:52 [INFO] - RT diff: -0.43205258698617244 2024-09-16 18:23:52 [INFO] - Fitting a mixture model... 2024-09-16 18:23:52 [INFO] - Matching-between-runs: CatC_0090_4... 2024-09-16 18:23:52 [INFO] - Calculating correlations between all other runs... 2024-09-16 18:23:52 [INFO] - Reading index from /home/nanopore-catalyst/HDD/mspms/raw_data/CatC_0090_4.quantindex 2024-09-16 18:23:52 [INFO] - Transferring CatA_0000_1... 2024-09-16 18:23:52 [INFO] - Transferring CatA_0000_2... 2024-09-16 18:23:52 [INFO] - Transferring CatA_0000_3... 2024-09-16 18:23:52 [INFO] - Transferring CatA_0000_4... 2024-09-16 18:23:52 [INFO] - Transferring CatC_0000_1... 2024-09-16 18:23:52 [INFO] - Transferring CatC_0000_2... 2024-09-16 18:23:52 [INFO] - Transferring CatC_0000_3... 2024-09-16 18:23:52 [INFO] - Transferring CatC_0000_4... 2024-09-16 18:23:52 [INFO] - Transferring CatC_0030_1... 2024-09-16 18:23:52 [INFO] - Transferring CatC_0030_2... 2024-09-16 18:23:52 [INFO] - Transferring CatC_0030_3... 2024-09-16 18:23:52 [INFO] - Transferring CatC_0030_4... 2024-09-16 18:23:52 [INFO] - Transferring CatC_0090_1... 2024-09-16 18:23:52 [INFO] - Transferring CatC_0090_2... 2024-09-16 18:23:52 [INFO] - Transferring CatC_0090_3... 2024-09-16 18:23:52 [INFO] - Training LDA models for all matched features. 2024-09-16 18:23:52 [INFO] - #{+1} = 316, #{-1} = 27, #{+2} = 1216, #{-2} = 104 2024-09-16 18:23:52 [INFO] - Standardized coefficients: 2024-09-16 18:23:52 [INFO] - log10(intensity): 0.650762891556673 2024-09-16 18:23:52 [INFO] - log10(KL): -0.5334263373078113 2024-09-16 18:23:52 [INFO] - abs(ppm): -0.39021963827531037 2024-09-16 18:23:52 [INFO] - RT diff: -0.4270800832397756 2024-09-16 18:23:52 [INFO] - Fitting a mixture model... 2024-09-16 18:23:52 [INFO] - Matching-between-runs: CatD_0000_1... 2024-09-16 18:23:52 [INFO] - Calculating correlations between all other runs... 2024-09-16 18:23:52 [INFO] - Reading index from /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0000_1.quantindex 2024-09-16 18:23:52 [INFO] - Transferring CatA_0000_1... 2024-09-16 18:23:52 [INFO] - Transferring CatA_0000_4... 2024-09-16 18:23:52 [INFO] - Transferring CatB_0000_1... 2024-09-16 18:23:52 [INFO] - Transferring CatB_0000_2... 2024-09-16 18:23:53 [INFO] - Transferring CatB_0000_3... 2024-09-16 18:23:53 [INFO] - Transferring CatC_0000_1... 2024-09-16 18:23:53 [INFO] - Transferring CatC_0000_2... 2024-09-16 18:23:53 [INFO] - Transferring CatC_0000_3... 2024-09-16 18:23:53 [INFO] - Transferring CatC_0000_4... 2024-09-16 18:23:53 [INFO] - Transferring CatC_0030_1... 2024-09-16 18:23:53 [INFO] - Transferring CatC_0030_3... 2024-09-16 18:23:53 [INFO] - Transferring CatC_0030_4... 2024-09-16 18:23:53 [INFO] - Transferring CatD_0000_2... 2024-09-16 18:23:53 [INFO] - Transferring CatD_0015_1... 2024-09-16 18:23:53 [INFO] - Transferring CatD_0015_4... 2024-09-16 18:23:53 [INFO] - Training LDA models for all matched features. 2024-09-16 18:23:53 [INFO] - #{+1} = 393, #{-1} = 39, #{+2} = 1095, #{-2} = 94 2024-09-16 18:23:53 [INFO] - Standardized coefficients: 2024-09-16 18:23:53 [INFO] - log10(intensity): 0.768983876801435 2024-09-16 18:23:53 [INFO] - log10(KL): -0.32856124189630737 2024-09-16 18:23:53 [INFO] - abs(ppm): -0.43236669058301197 2024-09-16 18:23:53 [INFO] - RT diff: -0.41224655186011055 2024-09-16 18:23:53 [INFO] - Fitting a mixture model... 2024-09-16 18:23:53 [INFO] - Matching-between-runs: CatD_0000_2... 2024-09-16 18:23:53 [INFO] - Calculating correlations between all other runs... 2024-09-16 18:23:53 [INFO] - Reading index from /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0000_2.quantindex 2024-09-16 18:23:53 [INFO] - Transferring CatA_0000_1... 2024-09-16 18:23:53 [INFO] - Transferring CatA_0000_4... 2024-09-16 18:23:53 [INFO] - Transferring CatB_0000_1... 2024-09-16 18:23:53 [INFO] - Transferring CatB_0000_2... 2024-09-16 18:23:53 [INFO] - Transferring CatB_0000_3... 2024-09-16 18:23:53 [INFO] - Transferring CatB_0000_4... 2024-09-16 18:23:53 [INFO] - Transferring CatC_0000_1... 2024-09-16 18:23:53 [INFO] - Transferring CatC_0000_2... 2024-09-16 18:23:53 [INFO] - Transferring CatC_0000_3... 2024-09-16 18:23:53 [INFO] - Transferring CatC_0000_4... 2024-09-16 18:23:53 [INFO] - Transferring CatC_0030_3... 2024-09-16 18:23:53 [INFO] - Transferring CatC_0030_4... 2024-09-16 18:23:53 [INFO] - Transferring CatD_0000_1... 2024-09-16 18:23:53 [INFO] - Transferring CatD_0015_1... 2024-09-16 18:23:53 [INFO] - Transferring CatD_0015_4... 2024-09-16 18:23:53 [INFO] - Training LDA models for all matched features. 2024-09-16 18:23:53 [INFO] - #{+1} = 425, #{-1} = 39, #{+2} = 1083, #{-2} = 88 2024-09-16 18:23:53 [INFO] - Standardized coefficients: 2024-09-16 18:23:53 [INFO] - log10(intensity): 0.8441137477495335 2024-09-16 18:23:53 [INFO] - log10(KL): -0.1096024877777055 2024-09-16 18:23:53 [INFO] - abs(ppm): -0.4698155315257766 2024-09-16 18:23:53 [INFO] - RT diff: -0.23395008414259408 2024-09-16 18:23:53 [INFO] - Fitting a mixture model... 2024-09-16 18:23:53 [INFO] - Matching-between-runs: CatD_0015_1... 2024-09-16 18:23:53 [INFO] - Calculating correlations between all other runs... 2024-09-16 18:23:53 [INFO] - Reading index from /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0015_1.quantindex 2024-09-16 18:23:53 [INFO] - Transferring CatA_0000_1... 2024-09-16 18:23:53 [INFO] - Transferring CatA_0000_2... 2024-09-16 18:23:53 [INFO] - Transferring CatA_0000_3... 2024-09-16 18:23:53 [INFO] - Transferring CatA_0000_4... 2024-09-16 18:23:53 [INFO] - Transferring CatB_0000_1... 2024-09-16 18:23:53 [INFO] - Transferring CatC_0000_1... 2024-09-16 18:23:53 [INFO] - Transferring CatC_0000_2... 2024-09-16 18:23:53 [INFO] - Transferring CatC_0000_3... 2024-09-16 18:23:53 [INFO] - Transferring CatC_0000_4... 2024-09-16 18:23:53 [INFO] - Transferring CatC_0030_4... 2024-09-16 18:23:53 [INFO] - Transferring CatD_0000_1... 2024-09-16 18:23:53 [INFO] - Transferring CatD_0000_2... 2024-09-16 18:23:53 [INFO] - Transferring CatD_0015_2... 2024-09-16 18:23:53 [INFO] - Transferring CatD_0015_3... 2024-09-16 18:23:53 [INFO] - Transferring CatD_0015_4... 2024-09-16 18:23:53 [INFO] - Training LDA models for all matched features. 2024-09-16 18:23:53 [INFO] - #{+1} = 429, #{-1} = 37, #{+2} = 1190, #{-2} = 109 2024-09-16 18:23:53 [INFO] - Standardized coefficients: 2024-09-16 18:23:53 [INFO] - log10(intensity): 0.760554261988033 2024-09-16 18:23:53 [INFO] - log10(KL): -0.3400908837882631 2024-09-16 18:23:53 [INFO] - abs(ppm): -0.4564975077421431 2024-09-16 18:23:53 [INFO] - RT diff: -0.3940192564759674 2024-09-16 18:23:53 [INFO] - Fitting a mixture model... 2024-09-16 18:23:53 [INFO] - Matching-between-runs: CatD_0015_2... 2024-09-16 18:23:53 [INFO] - Calculating correlations between all other runs... 2024-09-16 18:23:53 [INFO] - Reading index from /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0015_2.quantindex 2024-09-16 18:23:53 [INFO] - Transferring CatA_0000_1... 2024-09-16 18:23:53 [INFO] - Transferring CatA_0000_2... 2024-09-16 18:23:53 [INFO] - Transferring CatA_0000_3... 2024-09-16 18:23:53 [INFO] - Transferring CatA_0000_4... 2024-09-16 18:23:53 [INFO] - Transferring CatC_0000_1... 2024-09-16 18:23:53 [INFO] - Transferring CatC_0000_2... 2024-09-16 18:23:53 [INFO] - Transferring CatC_0000_3... 2024-09-16 18:23:53 [INFO] - Transferring CatC_0000_4... 2024-09-16 18:23:53 [INFO] - Transferring CatC_0030_3... 2024-09-16 18:23:54 [INFO] - Transferring CatC_0030_4... 2024-09-16 18:23:54 [INFO] - Transferring CatD_0000_1... 2024-09-16 18:23:54 [INFO] - Transferring CatD_0000_2... 2024-09-16 18:23:54 [INFO] - Transferring CatD_0015_1... 2024-09-16 18:23:54 [INFO] - Transferring CatD_0015_3... 2024-09-16 18:23:54 [INFO] - Transferring CatD_0015_4... 2024-09-16 18:23:54 [INFO] - Training LDA models for all matched features. 2024-09-16 18:23:54 [INFO] - #{+1} = 545, #{-1} = 60, #{+2} = 1063, #{-2} = 99 2024-09-16 18:23:54 [INFO] - Standardized coefficients: 2024-09-16 18:23:54 [INFO] - log10(intensity): 0.7983356256239849 2024-09-16 18:23:54 [INFO] - log10(KL): -0.49398924165250274 2024-09-16 18:23:54 [INFO] - abs(ppm): -0.35999777346514256 2024-09-16 18:23:54 [INFO] - RT diff: -0.24987100701276335 2024-09-16 18:23:54 [INFO] - Fitting a mixture model... 2024-09-16 18:23:54 [INFO] - Matching-between-runs: CatD_0015_3... 2024-09-16 18:23:54 [INFO] - Calculating correlations between all other runs... 2024-09-16 18:23:54 [INFO] - Reading index from /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0015_3.quantindex 2024-09-16 18:23:54 [INFO] - Transferring CatA_0000_1... 2024-09-16 18:23:54 [INFO] - Transferring CatA_0000_2... 2024-09-16 18:23:54 [INFO] - Transferring CatA_0000_3... 2024-09-16 18:23:54 [INFO] - Transferring CatA_0000_4... 2024-09-16 18:23:54 [INFO] - Transferring CatB_0000_1... 2024-09-16 18:23:54 [INFO] - Transferring CatB_0000_2... 2024-09-16 18:23:54 [INFO] - Transferring CatC_0000_1... 2024-09-16 18:23:54 [INFO] - Transferring CatC_0000_2... 2024-09-16 18:23:54 [INFO] - Transferring CatC_0000_3... 2024-09-16 18:23:54 [INFO] - Transferring CatC_0000_4... 2024-09-16 18:23:54 [INFO] - Transferring CatD_0000_1... 2024-09-16 18:23:54 [INFO] - Transferring CatD_0000_2... 2024-09-16 18:23:54 [INFO] - Transferring CatD_0015_1... 2024-09-16 18:23:54 [INFO] - Transferring CatD_0015_2... 2024-09-16 18:23:54 [INFO] - Transferring CatD_0015_4... 2024-09-16 18:23:54 [INFO] - Training LDA models for all matched features. 2024-09-16 18:23:54 [INFO] - #{+1} = 511, #{-1} = 48, #{+2} = 1121, #{-2} = 92 2024-09-16 18:23:54 [INFO] - Standardized coefficients: 2024-09-16 18:23:54 [INFO] - log10(intensity): 0.9026918004698883 2024-09-16 18:23:54 [INFO] - log10(KL): -0.20848362127145073 2024-09-16 18:23:54 [INFO] - abs(ppm): -0.25308736782252855 2024-09-16 18:23:54 [INFO] - RT diff: -0.27861959240986256 2024-09-16 18:23:54 [INFO] - Fitting a mixture model... 2024-09-16 18:23:54 [INFO] - Matching-between-runs: CatD_0015_4... 2024-09-16 18:23:54 [INFO] - Calculating correlations between all other runs... 2024-09-16 18:23:54 [INFO] - Reading index from /home/nanopore-catalyst/HDD/mspms/raw_data/CatD_0015_4.quantindex 2024-09-16 18:23:54 [INFO] - Transferring CatA_0000_1... 2024-09-16 18:23:54 [INFO] - Transferring CatB_0000_1... 2024-09-16 18:23:54 [INFO] - Transferring CatB_0000_2... 2024-09-16 18:23:54 [INFO] - Transferring CatB_0000_3... 2024-09-16 18:23:54 [INFO] - Transferring CatB_0000_4... 2024-09-16 18:23:54 [INFO] - Transferring CatC_0000_1... 2024-09-16 18:23:54 [INFO] - Transferring CatC_0000_2... 2024-09-16 18:23:54 [INFO] - Transferring CatC_0000_3... 2024-09-16 18:23:54 [INFO] - Transferring CatC_0000_4... 2024-09-16 18:23:54 [INFO] - Transferring CatC_0030_4... 2024-09-16 18:23:54 [INFO] - Transferring CatD_0000_1... 2024-09-16 18:23:54 [INFO] - Transferring CatD_0000_2... 2024-09-16 18:23:54 [INFO] - Transferring CatD_0015_1... 2024-09-16 18:23:54 [INFO] - Transferring CatD_0015_2... 2024-09-16 18:23:54 [INFO] - Transferring CatD_0015_3... 2024-09-16 18:23:54 [INFO] - Training LDA models for all matched features. 2024-09-16 18:23:54 [INFO] - #{+1} = 419, #{-1} = 46, #{+2} = 1226, #{-2} = 100 2024-09-16 18:23:54 [INFO] - Standardized coefficients: 2024-09-16 18:23:54 [INFO] - log10(intensity): 0.845900596454894 2024-09-16 18:23:54 [INFO] - log10(KL): -0.3382233195784933 2024-09-16 18:23:54 [INFO] - abs(ppm): -0.29479889820417066 2024-09-16 18:23:54 [INFO] - RT diff: -0.2883587637443427 2024-09-16 18:23:54 [INFO] - Fitting a mixture model... 2024-09-16 18:23:54 [INFO] - Estimating match-between-runs FDR... 2024-09-16 18:23:55 [INFO] - With ion FDR 0.010000, ion probability threshold is 0.971300 2024-09-16 18:23:55 [INFO] - With peptide FDR 1.000000, peptide probability threshold is -0.000100 2024-09-16 18:23:55 [INFO] - With protein FDR 1.000000, protein probability threshold is -0.000100 2024-09-16 18:23:55 [INFO] - Updating Philosopher's tables... 2024-09-16 18:23:57 [INFO] - Combining experiments and estimating protein intensity... 2024-09-16 18:23:59 [INFO] - Done! Process 'IonQuant' finished, exit code: 0 Please cite: (Any searches) MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics. Nat Methods 14:513 (2017) (Any searches) Fast deisotoping algorithm and its implementation in the MSFragger search engine. J. Proteome Res. 20:498 (2021) (timsTOF PASEF) Fast quantitative analysis of timsTOF PASEF data with MSFragger and IonQuant. Mol Cell Proteomics 19:1575 (2020) (Open search) Identification of modified peptides using localization-aware open search. Nat Commun. 11:4065 (2020) (Glyco search) Fast and comprehensive N- and O-glycoproteomics analysis with MSFragger-Glyco. Nat Methods 17:1125 (2020) (Labile search) MSFragger-Labile: A Flexible Method to Improve Labile PTM Analysis in Proteomics. Mol Cell Proteomics 22:100538 (2023) (MSBooster) MSBooster: improving peptide identification rates using deep learning-based features. Nat Commun. 14:4539 (2023) (PSM validation with Percolator) Semi-supervised learning for peptide identification from shotgun proteomics datasets. Nat Methods 4:923 (2007) (Protein inference with ProteinProphet)A statistical model for identifying proteins by tandem mass spectrometry. Anal. Chem. 75:4646 (2003) (FDR filtering and reporting) Philosopher: a versatile toolkit for shotgun proteomics data analysis. Nat Methods 17:869 (2020) (Label-free/isotopic-labeling quantification) IonQuant Enables Accurate and Sensitive Label-Free Quantification With FDR-Controlled Match-Between-Runs. Mol Cell Proteomics 20:100077 (2021) (Visualization with FragPipe-PDV) PDV: an integrative proteomics data viewer. Bioinformatics. 35(7):1249 (2019) =============================================================ALL JOBS DONE IN 26.7 MINUTES=============================================================