May-27 23:59:56.372 [main] DEBUG nextflow.cli.Launcher - $> nextflow run nf-core/nanoseq -r 3.1.0 -profile apptainer -w fei_second_run --max_time 48h --max_cpus 1 --max_memory 512GB --outdir fei_second_run --multiqc_title fei_nanopore_data_merged --input metadata/samplesheet_old.csv --skip_demultiplexing --skip_quantification --protocol DNA --call_variants -resume May-27 23:59:56.471 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W ~ version 24.04.1 May-27 23:59:56.489 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/div/pythagoras/u1/samuelc/.nextflow/plugins; core-plugins: nf-amazon@2.5.2,nf-azure@1.6.0,nf-cloudcache@0.4.1,nf-codecommit@0.2.0,nf-console@1.1.3,nf-ga4gh@1.3.0,nf-google@1.13.2,nf-tower@1.9.1,nf-wave@1.4.2 May-27 23:59:56.499 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: [] May-27 23:59:56.500 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: [] May-27 23:59:56.502 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.10.0 in 'deployment' mode May-27 23:59:56.514 [main] INFO org.pf4j.AbstractPluginManager - No plugins May-27 23:59:56.526 [main] DEBUG nextflow.scm.ProviderConfig - Using SCM config path: /div/pythagoras/u1/samuelc/.nextflow/scm May-27 23:59:57.301 [main] DEBUG nextflow.scm.AssetManager - Git config: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/nanoseq.git May-27 23:59:57.333 [main] DEBUG nextflow.scm.RepositoryFactory - Found Git repository result: [RepositoryFactory] May-27 23:59:57.343 [main] DEBUG nextflow.scm.AssetManager - Git config: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/nanoseq.git May-27 23:59:58.067 [main] DEBUG nextflow.config.ConfigBuilder - Found config home: /div/pythagoras/u1/samuelc/.nextflow/config May-27 23:59:58.069 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/nextflow.config May-27 23:59:58.071 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /div/pythagoras/u1/samuelc/.nextflow/config May-27 23:59:58.071 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/nextflow.config May-27 23:59:58.084 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /div/pythagoras/u1/samuelc/.nextflow/secrets/store.json May-27 23:59:58.086 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@459003a0] - activable => nextflow.secret.LocalSecretsProvider@459003a0 May-27 23:59:58.098 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `apptainer` May-27 23:59:58.127 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `apptainer` May-27 23:59:59.224 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [bih, cfc_dev, uzl_omics, ifb_core, denbi_qbic, alice, mjolnir_globe, uppmax, incliva, ilifu, uge, rosalind_uge, lugh, mccleary, unibe_ibu, vai, czbiohub_aws, jax, ccga_med, scw, unc_longleaf, tigem, tubingen_apg, google, apollo, ipop_up, vsc_calcua, pdc_kth, test_nodx_vc, googlels, daisybio, eddie, medair, biowulf, apptainer, bi, bigpurple, adcra, cedars, pawsey_setonix, vsc_kul_uhasselt, pawsey_nimbus, ucl_myriad, utd_ganymede, test_nodx_rnamod, charliecloud, icr_davros, ceres, munin, arm, rosalind, hasta, cfc, uzh, ebi_codon_slurm, ebc, ku_sund_dangpu, ccga_dx, crick, marvin, biohpc_gen, shifter, mana, mamba, york_viking, unc_lccc, wehi, awsbatch, wustl_htcf, arcc, imperial, maestro, software_license, utd_europa, genotoul, nci_gadi, abims, janelia, nu_genomics, googlebatch, oist, sahmri, mpcdf, leicester, vsc_ugent, create, sage, cambridge, jex, podman, ebi_codon, cheaha, xanadu, nyu_hpc, test, marjorie, computerome, ucd_sonic, seg_globe, sanger, dkfz, pasteur, einstein, ethz_euler, m3c, test_full, imb, ucl_cscluster, tuos_stanage, test_nodx_noaln, test_nodx_stringtie, azurebatch, hki, crukmi, csiro_petrichor, qmul_apocrita, docker, engaging, gis, hypatia, psmn, eva, nygc, fgcz, conda, crg, singularity, self_hosted_runner, tufts, uw_hyak_pedslabs, utd_sysbio, debug, genouest, cbe, phoenix, gitpod, seawulf, uod_hpc, fub_curta, uct_hpc, aws_tower, binac] May-27 23:59:59.276 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declaration May-27 23:59:59.276 [main] DEBUG nextflow.cli.CmdRun - Launching `https://github.com/nf-core/nanoseq` [voluminous_mayer] DSL2 - revision: 6e563e5436 [3.1.0] May-27 23:59:59.278 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[] May-27 23:59:59.279 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[] May-27 23:59:59.324 [main] DEBUG nextflow.Session - Session UUID: b3c8f1ba-8afb-4ba2-bd55-c79c30835e4a May-27 23:59:59.324 [main] DEBUG nextflow.Session - Run name: voluminous_mayer May-27 23:59:59.324 [main] DEBUG nextflow.Session - Executor pool size: 192 May-27 23:59:59.331 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null May-27 23:59:59.335 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=576; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false May-27 23:59:59.353 [main] DEBUG nextflow.cli.CmdRun - Version: 24.04.1 build 5913 Created: 20-05-2024 09:48 UTC (11:48 CEST) System: Linux 5.14.0-362.24.1.el9_3.x86_64 Runtime: Groovy 4.0.21 on OpenJDK 64-Bit Server VM 17.0.6+10 Encoding: UTF-8 (UTF-8) Process: 2606166@biotin4.hpc.uio.no [129.240.3.13] CPUs: 192 - Mem: 2 TB (307.5 GB) - Swap: 10 GB (9.5 GB) May-27 23:59:59.373 [main] DEBUG nextflow.Session - Work-dir: /storage/sahuarea/samuele_cancellieri/fei_nanopore/fei_second_run [xfs] May-27 23:59:59.404 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[] May-27 23:59:59.412 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory May-27 23:59:59.482 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory May-27 23:59:59.492 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 193; maxThreads: 1000 May-27 23:59:59.570 [main] DEBUG nextflow.Session - Session start May-27 23:59:59.573 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /storage/sahuarea/samuele_cancellieri/fei_nanopore/fei_second_run/pipeline_info/execution_trace_2024-05-27_23-59-58.txt May-27 23:59:59.579 [main] DEBUG nextflow.Session - Using default localLib path: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/lib May-27 23:59:59.583 [main] DEBUG nextflow.Session - Adding to the classpath library: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/lib May-27 23:59:59.583 [main] DEBUG nextflow.Session - Adding to the classpath library: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/lib/nfcore_external_java_deps.jar May-28 00:00:00.211 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution May-28 00:00:00.253 [main] INFO nextflow.Nextflow - ------------------------------------------------------ ,--./,-.  ___ __ __ __ ___ /,-._.--~'  |\ | |__ __ / ` / \ |__) |__ } {  | \| | \__, \__/ | \ |___ \`-._,-`-, `._,._,'  nf-core/nanoseq v3.1.0-g6e563e5 ------------------------------------------------------ Core Nextflow options revision : 3.1.0 runName : voluminous_mayer containerEngine : apptainer launchDir : /storage/sahuarea/samuele_cancellieri/fei_nanopore workDir : /storage/sahuarea/samuele_cancellieri/fei_nanopore/fei_second_run projectDir : /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq userName : samuelc profile : apptainer configFiles : /div/pythagoras/u1/samuelc/.nextflow/config, /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/nextflow.config Input/output options input : metadata/samplesheet_old.csv protocol : DNA outdir : fei_second_run multiqc_title : fei_nanopore_data_merged Demultiplexing options skip_demultiplexing: true Variant calling options call_variants : true Differential analysis options skip_quantification: true RNA fusion analysis options jaffal_ref_dir : null Reference genome options igenomes_base : s3://ngi-igenomes/igenomes/ Max job request options max_cpus : 1 max_memory : 512GB max_time : 48h !! Only displaying parameters that differ from the pipeline defaults !! ------------------------------------------------------ If you use nf-core/nanoseq for your analysis please cite: * The pipeline https://doi.org/10.5281/zenodo.5740870 * The nf-core framework https://doi.org/10.1038/s41587-020-0439-x * Software dependencies https://github.com/nf-core/nanoseq/blob/master/CITATIONS.md ------------------------------------------------------ May-28 00:00:00.775 [main] WARN nextflow.script.ScriptBinding - Access to undefined parameter `enable_conda` -- Initialise it to a default value eg. `params.enable_conda = some_value` May-28 00:00:03.136 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_NANOSEQ:NANOSEQ:INPUT_CHECK:SAMPLESHEET_CHECK May-28 00:00:03.138 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMPLESHEET_CHECK` matches process NFCORE_NANOSEQ:NANOSEQ:INPUT_CHECK:SAMPLESHEET_CHECK May-28 00:00:03.151 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-28 00:00:03.151 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-28 00:00:03.156 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local May-28 00:00:03.160 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=192; memory=2 TB; capacity=192; pollInterval=100ms; dumpInterval=5m May-28 00:00:03.162 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local) May-28 00:00:03.258 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_NANOSEQ:NANOSEQ:QCFASTQ_NANOPLOT_FASTQC:NANOPLOT May-28 00:00:03.259 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:NANOPLOT` matches process NFCORE_NANOSEQ:NANOSEQ:QCFASTQ_NANOPLOT_FASTQC:NANOPLOT May-28 00:00:03.264 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-28 00:00:03.264 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-28 00:00:03.273 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_NANOSEQ:NANOSEQ:QCFASTQ_NANOPLOT_FASTQC:FASTQC May-28 00:00:03.274 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:FASTQC` matches process NFCORE_NANOSEQ:NANOSEQ:QCFASTQ_NANOPLOT_FASTQC:FASTQC May-28 00:00:03.278 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-28 00:00:03.278 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-28 00:00:03.306 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_NANOSEQ:NANOSEQ:PREPARE_GENOME:GET_CHROM_SIZES May-28 00:00:03.307 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GET_CHROM_SIZES` matches process NFCORE_NANOSEQ:NANOSEQ:PREPARE_GENOME:GET_CHROM_SIZES May-28 00:00:03.309 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-28 00:00:03.309 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-28 00:00:03.326 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_NANOSEQ:NANOSEQ:PREPARE_GENOME:GTF2BED May-28 00:00:03.327 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:GTF2BED` matches process NFCORE_NANOSEQ:NANOSEQ:PREPARE_GENOME:GTF2BED May-28 00:00:03.329 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-28 00:00:03.329 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-28 00:00:03.357 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_NANOSEQ:NANOSEQ:PREPARE_GENOME:SAMTOOLS_FAIDX May-28 00:00:03.358 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_FAIDX` matches process NFCORE_NANOSEQ:NANOSEQ:PREPARE_GENOME:SAMTOOLS_FAIDX May-28 00:00:03.360 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-28 00:00:03.360 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-28 00:00:03.376 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_NANOSEQ:NANOSEQ:ALIGN_MINIMAP2:MINIMAP2_INDEX May-28 00:00:03.377 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MINIMAP2_INDEX` matches process NFCORE_NANOSEQ:NANOSEQ:ALIGN_MINIMAP2:MINIMAP2_INDEX May-28 00:00:03.379 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-28 00:00:03.379 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-28 00:00:03.390 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_NANOSEQ:NANOSEQ:ALIGN_MINIMAP2:MINIMAP2_ALIGN May-28 00:00:03.391 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MINIMAP2_ALIGN` matches process NFCORE_NANOSEQ:NANOSEQ:ALIGN_MINIMAP2:MINIMAP2_ALIGN May-28 00:00:03.394 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-28 00:00:03.394 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-28 00:00:03.404 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_NANOSEQ:NANOSEQ:BAM_SORT_INDEX_SAMTOOLS:SAMTOOLS_VIEW_BAM May-28 00:00:03.404 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_VIEW_BAM` matches process NFCORE_NANOSEQ:NANOSEQ:BAM_SORT_INDEX_SAMTOOLS:SAMTOOLS_VIEW_BAM May-28 00:00:03.406 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-28 00:00:03.406 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-28 00:00:03.412 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name NFCORE_NANOSEQ:NANOSEQ:BAM_SORT_INDEX_SAMTOOLS:SAMTOOLS_SORT_INDEX May-28 00:00:03.412 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_SORT_INDEX` matches process NFCORE_NANOSEQ:NANOSEQ:BAM_SORT_INDEX_SAMTOOLS:SAMTOOLS_SORT_INDEX May-28 00:00:03.414 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-28 00:00:03.414 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-28 00:00:03.426 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_NANOSEQ:NANOSEQ:BAM_SORT_INDEX_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS May-28 00:00:03.426 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_STATS` matches process NFCORE_NANOSEQ:NANOSEQ:BAM_SORT_INDEX_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS May-28 00:00:03.428 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-28 00:00:03.428 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-28 00:00:03.433 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_NANOSEQ:NANOSEQ:BAM_SORT_INDEX_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT May-28 00:00:03.433 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_FLAGSTAT` matches process NFCORE_NANOSEQ:NANOSEQ:BAM_SORT_INDEX_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT May-28 00:00:03.435 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-28 00:00:03.435 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-28 00:00:03.439 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_NANOSEQ:NANOSEQ:BAM_SORT_INDEX_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS May-28 00:00:03.439 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SAMTOOLS_IDXSTATS` matches process NFCORE_NANOSEQ:NANOSEQ:BAM_SORT_INDEX_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS May-28 00:00:03.441 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-28 00:00:03.441 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-28 00:00:03.461 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_NANOSEQ:NANOSEQ:SHORT_VARIANT_CALLING:MEDAKA_VARIANT May-28 00:00:03.461 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MEDAKA_VARIANT` matches process NFCORE_NANOSEQ:NANOSEQ:SHORT_VARIANT_CALLING:MEDAKA_VARIANT May-28 00:00:03.463 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-28 00:00:03.463 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-28 00:00:03.472 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_NANOSEQ:NANOSEQ:SHORT_VARIANT_CALLING:MEDAKA_BGZIP_VCF May-28 00:00:03.473 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MEDAKA_BGZIP_VCF` matches process NFCORE_NANOSEQ:NANOSEQ:SHORT_VARIANT_CALLING:MEDAKA_BGZIP_VCF May-28 00:00:03.475 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-28 00:00:03.475 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-28 00:00:03.482 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_NANOSEQ:NANOSEQ:SHORT_VARIANT_CALLING:MEDAKA_TABIX_VCF May-28 00:00:03.484 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MEDAKA_TABIX_VCF` matches process NFCORE_NANOSEQ:NANOSEQ:SHORT_VARIANT_CALLING:MEDAKA_TABIX_VCF May-28 00:00:03.486 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-28 00:00:03.486 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-28 00:00:03.501 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_high` matches labels `process_high` for process with name NFCORE_NANOSEQ:NANOSEQ:STRUCTURAL_VARIANT_CALLING:SNIFFLES May-28 00:00:03.502 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SNIFFLES` matches process NFCORE_NANOSEQ:NANOSEQ:STRUCTURAL_VARIANT_CALLING:SNIFFLES May-28 00:00:03.504 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-28 00:00:03.504 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-28 00:00:03.510 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_NANOSEQ:NANOSEQ:STRUCTURAL_VARIANT_CALLING:SNIFFLES_SORT_VCF May-28 00:00:03.511 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SNIFFLES_SORT_VCF` matches process NFCORE_NANOSEQ:NANOSEQ:STRUCTURAL_VARIANT_CALLING:SNIFFLES_SORT_VCF May-28 00:00:03.512 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-28 00:00:03.512 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-28 00:00:03.519 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_NANOSEQ:NANOSEQ:STRUCTURAL_VARIANT_CALLING:SNIFFLES_TABIX_VCF May-28 00:00:03.520 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:SNIFFLES_TABIX_VCF` matches process NFCORE_NANOSEQ:NANOSEQ:STRUCTURAL_VARIANT_CALLING:SNIFFLES_TABIX_VCF May-28 00:00:03.522 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-28 00:00:03.522 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-28 00:00:03.531 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_NANOSEQ:NANOSEQ:BEDTOOLS_UCSC_BIGWIG:BEDTOOLS_GENOMECOV May-28 00:00:03.532 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BEDTOOLS_GENOMECOV` matches process NFCORE_NANOSEQ:NANOSEQ:BEDTOOLS_UCSC_BIGWIG:BEDTOOLS_GENOMECOV May-28 00:00:03.533 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-28 00:00:03.533 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-28 00:00:03.537 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_NANOSEQ:NANOSEQ:BEDTOOLS_UCSC_BIGWIG:UCSC_BEDGRAPHTOBIGWIG May-28 00:00:03.538 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UCSC_BEDGRAPHTOBIGWIG` matches process NFCORE_NANOSEQ:NANOSEQ:BEDTOOLS_UCSC_BIGWIG:UCSC_BEDGRAPHTOBIGWIG May-28 00:00:03.540 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-28 00:00:03.540 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-28 00:00:03.551 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_NANOSEQ:NANOSEQ:BEDTOOLS_UCSC_BIGBED:BEDTOOLS_BAMBED May-28 00:00:03.551 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:BEDTOOLS_BAMBED` matches process NFCORE_NANOSEQ:NANOSEQ:BEDTOOLS_UCSC_BIGBED:BEDTOOLS_BAMBED May-28 00:00:03.553 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-28 00:00:03.553 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-28 00:00:03.557 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_NANOSEQ:NANOSEQ:BEDTOOLS_UCSC_BIGBED:UCSC_BED12TOBIGBED May-28 00:00:03.557 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:UCSC_BED12TOBIGBED` matches process NFCORE_NANOSEQ:NANOSEQ:BEDTOOLS_UCSC_BIGBED:UCSC_BED12TOBIGBED May-28 00:00:03.559 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-28 00:00:03.559 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-28 00:00:03.592 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_NANOSEQ:NANOSEQ:CUSTOM_DUMPSOFTWAREVERSIONS May-28 00:00:03.593 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:CUSTOM_DUMPSOFTWAREVERSIONS` matches process NFCORE_NANOSEQ:NANOSEQ:CUSTOM_DUMPSOFTWAREVERSIONS May-28 00:00:03.595 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-28 00:00:03.595 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-28 00:00:03.614 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_NANOSEQ:NANOSEQ:MULTIQC May-28 00:00:03.614 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:MULTIQC` matches process NFCORE_NANOSEQ:NANOSEQ:MULTIQC May-28 00:00:03.617 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null May-28 00:00:03.617 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' May-28 00:00:03.621 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: SNIFFLES_TABIX_VCF, BAMBU, NFCORE_NANOSEQ:NANOSEQ:ALIGN_MINIMAP2:MINIMAP2_INDEX, NFCORE_NANOSEQ:NANOSEQ:BAM_SORT_INDEX_SAMTOOLS:SAMTOOLS_SORT_INDEX, NFCORE_NANOSEQ:NANOSEQ:BAM_SORT_INDEX_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT, NFCORE_NANOSEQ:NANOSEQ:STRUCTURAL_VARIANT_CALLING:SNIFFLES, SAMTOOLS_SORT_INDEX, TABIX_BGZIP, NFCORE_NANOSEQ:NANOSEQ:BEDTOOLS_UCSC_BIGWIG:BEDTOOLS_GENOMECOV, NANOPOLISH_INDEX_EVENTALIGN, M6ANET_DATAPREP, XPORE_DIFFMOD, DEXSEQ, SNIFFLES, GET_JAFFAL_REF, SAMTOOLS_STATS, UNTAR, NFCORE_NANOSEQ:NANOSEQ:QCFASTQ_NANOPLOT_FASTQC:FASTQC, NFCORE_NANOSEQ:NANOSEQ:INPUT_CHECK:SAMPLESHEET_CHECK, NFCORE_NANOSEQ:NANOSEQ:PREPARE_GENOME:GET_CHROM_SIZES, NFCORE_NANOSEQ:NANOSEQ:STRUCTURAL_VARIANT_CALLING:SNIFFLES_TABIX_VCF, SNIFFLES_SORT_VCF, NFCORE_NANOSEQ:NANOSEQ:MULTIQC, DESEQ2, UCSC_BED12TOBIGBED, GRAPHMAP2_ALIGN, BEDTOOLS_GENOMECOV, PEPPER_MARGIN_DEEPVARIANT, NFCORE_NANOSEQ:NANOSEQ:BEDTOOLS_UCSC_BIGWIG:UCSC_BEDGRAPHTOBIGWIG, CUTESV, NFCORE_NANOSEQ:NANOSEQ:BAM_SORT_INDEX_SAMTOOLS:SAMTOOLS_VIEW_BAM, NFCORE_NANOSEQ:NANOSEQ:PREPARE_GENOME:SAMTOOLS_FAIDX, NFCORE_NANOSEQ:NANOSEQ:PREPARE_GENOME:GTF2BED, DEEPVARIANT_TABIX_GVCF, DEEPVARIANT, CUTESV_TABIX_VCF, NFCORE_NANOSEQ:NANOSEQ:BEDTOOLS_UCSC_BIGBED:UCSC_BED12TOBIGBED, NANOPLOT, MINIMAP2_INDEX, SAMTOOLS_INDEX, DEEPVARIANT_TABIX_VCF, MEDAKA_BGZIP_VCF, TABIX_TABIX, FASTQC, GRAPHMAP2_INDEX, NFCORE_NANOSEQ:NANOSEQ:SHORT_VARIANT_CALLING:MEDAKA_TABIX_VCF, NFCORE_NANOSEQ:NANOSEQ:STRUCTURAL_VARIANT_CALLING:SNIFFLES_SORT_VCF, UCSC_BEDGRAPHTOBIGWIG, NFCORE_NANOSEQ:NANOSEQ:BEDTOOLS_UCSC_BIGBED:BEDTOOLS_BAMBED, MULTIQC, GTF2BED, NFCORE_NANOSEQ:NANOSEQ:CUSTOM_DUMPSOFTWAREVERSIONS, STRINGTIE_MERGE, BEDTOOLS_BAMBED, SAMTOOLS_SORT, SUBREAD_FEATURECOUNTS, GET_CHROM_SIZES, NFCORE_NANOSEQ:NANOSEQ:BAM_SORT_INDEX_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS, M6ANET_INFERENCE, JAFFAL, NFCORE_NANOSEQ:NANOSEQ:SHORT_VARIANT_CALLING:MEDAKA_BGZIP_VCF, SAMTOOLS_FAIDX, NFCORE_NANOSEQ:NANOSEQ:ALIGN_MINIMAP2:MINIMAP2_ALIGN, CUTESV_SORT_VCF, QCAT, SAMTOOLS_FLAGSTAT, SAMPLESHEET_CHECK, XPORE_DATAPREP, SNIFFLES_BGZIP_VCF, STRINGTIE2, BCFTOOLS_SORT, CUTESV_BGZIP_VCF, NFCORE_NANOSEQ:NANOSEQ:BAM_SORT_INDEX_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS, MEDAKA_TABIX_VCF, SAMTOOLS_VIEW_BAM, GET_TEST_DATA, NFCORE_NANOSEQ:NANOSEQ:QCFASTQ_NANOPLOT_FASTQC:NANOPLOT, GET_NANOLYSE_FASTA, NANOLYSE, MEDAKA_VARIANT, BAM_RENAME, SAMTOOLS_IDXSTATS, NFCORE_NANOSEQ:NANOSEQ:SHORT_VARIANT_CALLING:MEDAKA_VARIANT, MINIMAP2_ALIGN, CUSTOM_DUMPSOFTWAREVERSIONS May-28 00:00:03.632 [main] DEBUG nextflow.Session - Igniting dataflow network (50) May-28 00:00:03.632 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_NANOSEQ:NANOSEQ:INPUT_CHECK:SAMPLESHEET_CHECK May-28 00:00:03.633 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_NANOSEQ:NANOSEQ:QCFASTQ_NANOPLOT_FASTQC:NANOPLOT May-28 00:00:03.634 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_NANOSEQ:NANOSEQ:QCFASTQ_NANOPLOT_FASTQC:FASTQC May-28 00:00:03.634 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_NANOSEQ:NANOSEQ:PREPARE_GENOME:GET_CHROM_SIZES May-28 00:00:03.634 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_NANOSEQ:NANOSEQ:PREPARE_GENOME:GTF2BED May-28 00:00:03.635 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_NANOSEQ:NANOSEQ:PREPARE_GENOME:SAMTOOLS_FAIDX May-28 00:00:03.635 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_NANOSEQ:NANOSEQ:ALIGN_MINIMAP2:MINIMAP2_INDEX May-28 00:00:03.635 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_NANOSEQ:NANOSEQ:ALIGN_MINIMAP2:MINIMAP2_ALIGN May-28 00:00:03.635 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_NANOSEQ:NANOSEQ:BAM_SORT_INDEX_SAMTOOLS:SAMTOOLS_VIEW_BAM May-28 00:00:03.636 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_NANOSEQ:NANOSEQ:BAM_SORT_INDEX_SAMTOOLS:SAMTOOLS_SORT_INDEX May-28 00:00:03.636 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_NANOSEQ:NANOSEQ:BAM_SORT_INDEX_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS May-28 00:00:03.636 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_NANOSEQ:NANOSEQ:BAM_SORT_INDEX_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT May-28 00:00:03.636 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_NANOSEQ:NANOSEQ:BAM_SORT_INDEX_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS May-28 00:00:03.637 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_NANOSEQ:NANOSEQ:SHORT_VARIANT_CALLING:MEDAKA_VARIANT May-28 00:00:03.638 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_NANOSEQ:NANOSEQ:SHORT_VARIANT_CALLING:MEDAKA_BGZIP_VCF May-28 00:00:03.638 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_NANOSEQ:NANOSEQ:SHORT_VARIANT_CALLING:MEDAKA_TABIX_VCF May-28 00:00:03.639 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_NANOSEQ:NANOSEQ:STRUCTURAL_VARIANT_CALLING:SNIFFLES May-28 00:00:03.639 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_NANOSEQ:NANOSEQ:STRUCTURAL_VARIANT_CALLING:SNIFFLES_SORT_VCF May-28 00:00:03.639 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_NANOSEQ:NANOSEQ:STRUCTURAL_VARIANT_CALLING:SNIFFLES_TABIX_VCF May-28 00:00:03.640 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_NANOSEQ:NANOSEQ:BEDTOOLS_UCSC_BIGWIG:BEDTOOLS_GENOMECOV May-28 00:00:03.640 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_NANOSEQ:NANOSEQ:BEDTOOLS_UCSC_BIGWIG:UCSC_BEDGRAPHTOBIGWIG May-28 00:00:03.641 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_NANOSEQ:NANOSEQ:BEDTOOLS_UCSC_BIGBED:BEDTOOLS_BAMBED May-28 00:00:03.641 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_NANOSEQ:NANOSEQ:BEDTOOLS_UCSC_BIGBED:UCSC_BED12TOBIGBED May-28 00:00:03.641 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_NANOSEQ:NANOSEQ:CUSTOM_DUMPSOFTWAREVERSIONS May-28 00:00:03.642 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_NANOSEQ:NANOSEQ:MULTIQC May-28 00:00:03.643 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files: Script_bc87ae5ad864b5ca: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/./workflows/../subworkflows/local/../../modules/local/ucsc_bedgraphtobigwig.nf Script_baaa2e5a3f9c0763: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/./workflows/../subworkflows/local/align_minimap2.nf Script_9147fc2e9bf0c6a5: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/./workflows/../subworkflows/local/../../modules/local/xpore_diffmod.nf Script_392e714dbe8a1df6: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/./workflows/../subworkflows/local/../../modules/nf-core/fastqc/main.nf Script_0c1ca5ef7dc6c642: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/./workflows/../modules/local/bam_rename.nf Script_505ec9861459c120: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/./workflows/../subworkflows/local/../../modules/nf-core/tabix/bgzip/main.nf Script_a68d5feb9279c11c: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/./workflows/../subworkflows/local/../../modules/local/m6anet_dataprep.nf Script_fc41373a5d7d5bfa: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/./workflows/../modules/local/bambu.nf Script_c701dffdd78c77be: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/./workflows/../subworkflows/local/../../modules/local/get_chrom_sizes.nf Script_fc3d4f6b4e02cfe9: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/./workflows/../subworkflows/local/../../modules/local/minimap2_index.nf Script_0d565de2ba87d6c8: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/./workflows/../subworkflows/local/../../modules/local/jaffal.nf Script_56314d2c57757f2a: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/./workflows/../subworkflows/local/../../modules/local/nanopolish_index_eventalign.nf Script_9f5759e89bdbf53f: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/./workflows/../subworkflows/local/../../modules/local/minimap2_align.nf Script_5f3a0549c5575017: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/./workflows/../subworkflows/local/qcfastq_nanoplot_fastqc.nf Script_08e8120406c42c87: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/./workflows/../subworkflows/local/../../subworkflows/nf-core/../../modules/nf-core/samtools/stats/main.nf Script_cb211c549341a328: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/./workflows/../subworkflows/local/../../subworkflows/nf-core/../../modules/nf-core/samtools/idxstats/main.nf Script_ece15101865d8f4a: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/./workflows/nanoseq.nf Script_d499d47010ed84a6: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/./workflows/../subworkflows/local/../../modules/local/dexseq.nf Script_e332896fb6593c29: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/./workflows/../subworkflows/local/../../modules/local/stringtie2.nf Script_1acc6c07bdc27d33: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/./workflows/../subworkflows/local/../../modules/local/medaka_variant.nf Script_3ed7cdfd5cf5f414: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/./workflows/../modules/local/get_nanolyse_fasta.nf Script_9a38ee04b01174ab: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/./workflows/../modules/local/get_test_data.nf Script_5a936eec0a0d6fae: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/./workflows/../subworkflows/local/../../modules/local/get_jaffal_ref.nf Script_92c226a4b8189b23: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/./workflows/../subworkflows/local/../../modules/local/ucsc_bed12tobigbed.nf Script_abf9087b1c4fde5e: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/./workflows/../subworkflows/local/../../modules/local/cutesv.nf Script_aa204f00e460a490: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/./workflows/../subworkflows/local/../../modules/local/deepvariant.nf Script_4af3f2569d318659: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/./workflows/../subworkflows/local/../../modules/local/gtf2bed.nf Script_1aa52c5cc59dfaa8: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/./workflows/../modules/local/multiqc.nf Script_a063e9fdaa49ec58: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/./workflows/../subworkflows/local/../../subworkflows/nf-core/bam_stats_samtools.nf Script_813f8bd24f68044c: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/./workflows/../subworkflows/local/../../subworkflows/nf-core/../../modules/nf-core/samtools/flagstat/main.nf Script_3e5bd3bd630cb772: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/./workflows/../modules/nf-core/nanolyse/main.nf Script_622d4b2a91e75ea6: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/./workflows/../subworkflows/local/../../modules/nf-core/samtools/index/main.nf Script_c45bc812e1d5f5cb: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/./workflows/../subworkflows/local/../../modules/nf-core/samtools/sort/main.nf Script_a552269934e8d8de: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/./workflows/../subworkflows/local/../../modules/nf-core/samtools/faidx/main.nf Script_71a3b5208ae2d2c1: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/./workflows/../subworkflows/local/../../modules/local/xpore_dataprep.nf Script_dd40e7ee19caedbd: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/./workflows/../subworkflows/local/../../modules/nf-core/tabix/tabix/main.nf Script_756fb404e3a86813: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/./workflows/../subworkflows/local/bedtools_ucsc_bigwig.nf Script_a2889bb270434f37: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/./workflows/../subworkflows/local/short_variant_calling.nf Script_cdf3da412293fa45: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/./workflows/../subworkflows/local/../../modules/nf-core/untar/main.nf Script_96579e44a6e66cf3: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/main.nf Script_bfc43472a62a96bf: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/./workflows/../subworkflows/local/../../modules/local/samplesheet_check.nf Script_2ebc0fec72e677cc: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/./workflows/../subworkflows/local/../../modules/local/graphmap2_align.nf Script_400f660dc919fb65: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/./workflows/../subworkflows/local/align_graphmap2.nf Script_73d7fefc55c924d3: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/./workflows/../subworkflows/local/input_check.nf Script_5b3c40854b745bc1: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/./workflows/../subworkflows/local/quantify_stringtie_featurecounts.nf Script_aa73f213cf4c1a39: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/./workflows/../subworkflows/local/rna_modifications_xpore_m6anet.nf Script_1410347fabfe4819: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/./workflows/../subworkflows/local/../../modules/local/samtools_sort_index.nf Script_09e1dc2cabbac8a7: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/./workflows/../subworkflows/local/prepare_genome.nf Script_51f1a671ca2d31cc: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/./workflows/../subworkflows/local/bam_sort_index_samtools.nf Script_57e2107c0843bbed: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/./workflows/../subworkflows/local/../../modules/local/deseq2.nf Script_aef0aa072b959756: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/./workflows/../subworkflows/local/../../modules/nf-core/bcftools/sort/main.nf Script_0fe890aec39cf994: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/./workflows/../subworkflows/local/../../modules/local/samtools_view_bam.nf Script_470d462c1256120a: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/./workflows/../modules/local/qcat.nf Script_b2317a11268bd508: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/./workflows/../subworkflows/local/../../modules/local/m6anet_inference.nf Script_ac86f64dd61924c5: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/./workflows/../subworkflows/local/bedtools_ucsc_bigbed.nf Script_b1fdbee1932eafb4: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/./workflows/../subworkflows/local/../../modules/local/pepper_margin_deepvariant.nf Script_dc576499bdaf05f8: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/./workflows/../modules/nf-core/custom/dumpsoftwareversions/main.nf Script_ee1ef9ec05ecaeb5: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/./workflows/../subworkflows/local/../../modules/local/graphmap2_index.nf Script_ec08d50709821cef: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/./workflows/../subworkflows/local/../../modules/local/bedtools_bamtobed.nf Script_0a2bd97c11252c13: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/./workflows/../subworkflows/local/../../modules/nf-core/nanoplot/main.nf Script_281ca4766407b903: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/./workflows/../subworkflows/local/rna_fusions_jaffal.nf Script_71b1bd40ad956ee9: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/./workflows/../subworkflows/local/../../modules/local/subread_featurecounts.nf Script_77c74b582a9f373a: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/./workflows/../subworkflows/local/../../modules/nf-core/stringtie/merge/main.nf Script_c5b0da1b34408130: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/./workflows/../subworkflows/local/differential_deseq2_dexseq.nf Script_dd9e93ab6d097c8c: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/./workflows/../subworkflows/local/structural_variant_calling.nf Script_875bce8dda01a9f7: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/./workflows/../subworkflows/local/../../modules/local/bedtools_genomecov.nf Script_3cab1dda38cc3727: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/./workflows/../subworkflows/local/../../modules/local/sniffles.nf May-28 00:00:03.643 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination May-28 00:00:03.643 [main] DEBUG nextflow.Session - Session await May-28 00:00:03.691 [Actor Thread 181] DEBUG nextflow.container.SingularityCache - Apptainer found local store for image=docker://quay.io/biocontainers/python:3.8.3; path=/storage/sahuarea/samuele_cancellieri/apptainer_cache/quay.io-biocontainers-python-3.8.3.img May-28 00:00:03.710 [Actor Thread 162] DEBUG nextflow.util.HashBuilder - Hash asset file sha-256: /div/pythagoras/u1/samuelc/.nextflow/assets/nf-core/nanoseq/bin/check_samplesheet.py May-28 00:00:03.715 [Actor Thread 179] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.001 s; external sort time: 0.01 s; total time: 0.011 s May-28 00:00:03.715 [Actor Thread 179] DEBUG nextflow.file.FileCollector - >> temp file exists? false May-28 00:00:03.716 [Actor Thread 179] DEBUG nextflow.file.FileCollector - Missed collect-file cache -- cause: java.nio.file.NoSuchFileException: /storage/sahuarea/samuele_cancellieri/fei_nanopore/fei_second_run/collect-file/1b151f8fb3c2a7ad7133b70faa1b12db May-28 00:00:03.720 [Actor Thread 179] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /storage/sahuarea/samuele_cancellieri/fei_nanopore/fei_second_run/collect-file/1b151f8fb3c2a7ad7133b70faa1b12db May-28 00:00:03.727 [Actor Thread 179] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /storage/sahuarea/samuele_cancellieri/general_tmp/nxf-13032752406872764631 May-28 00:00:03.745 [Actor Thread 162] INFO nextflow.processor.TaskProcessor - [e6/0c2698] Cached process > NFCORE_NANOSEQ:NANOSEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet_old.csv) May-28 00:00:03.764 [Actor Thread 186] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-amazon version: 2.5.2 May-28 00:00:03.771 [Actor Thread 162] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'PublishDir' minSize=10; maxSize=576; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false May-28 00:00:03.781 [Actor Thread 186] INFO org.pf4j.AbstractPluginManager - Plugin 'nf-amazon@2.5.2' resolved May-28 00:00:03.781 [Actor Thread 186] INFO org.pf4j.AbstractPluginManager - Start plugin 'nf-amazon@2.5.2' May-28 00:00:03.801 [Actor Thread 186] DEBUG nextflow.plugin.BasePlugin - Plugin started nf-amazon@2.5.2 May-28 00:00:03.815 [Actor Thread 186] DEBUG nextflow.file.FileHelper - > Added 'S3FileSystemProvider' to list of installed providers [s3] May-28 00:00:03.815 [Actor Thread 186] DEBUG nextflow.file.FileHelper - Started plugin 'nf-amazon' required to handle file: s3://ngi-igenomes/igenomes//Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa May-28 00:00:03.822 [Actor Thread 186] DEBUG nextflow.file.FileHelper - Creating a file system instance for provider: S3FileSystemProvider May-28 00:00:03.832 [Actor Thread 186] DEBUG nextflow.cloud.aws.config.AwsConfig - AWS S3 config properties: {max_error_retry=5} May-28 00:00:06.218 [Actor Thread 186] DEBUG n.c.aws.util.S3CredentialsProvider - No AWS credentials available - falling back to anonymous access May-28 00:00:06.754 [Actor Thread 192] DEBUG nextflow.container.SingularityCache - Apptainer found local store for image=docker://quay.io/biocontainers/nanoplot:1.41.0--pyhdfd78af_0; path=/storage/sahuarea/samuele_cancellieri/apptainer_cache/quay.io-biocontainers-nanoplot-1.41.0--pyhdfd78af_0.img May-28 00:00:06.754 [Actor Thread 183] DEBUG nextflow.container.SingularityCache - Apptainer found local store for image=docker://quay.io/biocontainers/fastqc:0.11.9--0; path=/storage/sahuarea/samuele_cancellieri/apptainer_cache/quay.io-biocontainers-fastqc-0.11.9--0.img May-28 00:00:06.764 [Actor Thread 162] INFO nextflow.processor.TaskProcessor - [fe/f5c15b] Cached process > NFCORE_NANOSEQ:NANOSEQ:QCFASTQ_NANOPLOT_FASTQC:FASTQC (WT_R1) May-28 00:00:06.767 [Actor Thread 185] INFO nextflow.processor.TaskProcessor - [e5/2a0591] Cached process > NFCORE_NANOSEQ:NANOSEQ:QCFASTQ_NANOPLOT_FASTQC:NANOPLOT (WT_R1) May-28 00:00:06.831 [Actor Thread 185] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_NANOSEQ:NANOSEQ:QCFASTQ_NANOPLOT_FASTQC:NANOPLOT > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> May-28 00:00:06.968 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Local cache found for foreign file s3://ngi-igenomes/igenomes/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa at /storage/sahuarea/samuele_cancellieri/fei_nanopore/fei_second_run/stage-b3c8f1ba-8afb-4ba2-bd55-c79c30835e4a/a1/e29db5c0006096304c4540c90cb2aa/genome.fa May-28 00:00:06.972 [Actor Thread 162] DEBUG nextflow.container.SingularityCache - Apptainer found local store for image=docker://quay.io/biocontainers/samtools:1.16.1--h6899075_1; path=/storage/sahuarea/samuele_cancellieri/apptainer_cache/quay.io-biocontainers-samtools-1.16.1--h6899075_1.img May-28 00:00:06.972 [Actor Thread 187] DEBUG nextflow.container.SingularityCache - Apptainer found local store for image=docker://quay.io/biocontainers/samtools:1.13--h8c37831_0; path=/storage/sahuarea/samuele_cancellieri/apptainer_cache/quay.io-biocontainers-samtools-1.13--h8c37831_0.img May-28 00:00:06.983 [Actor Thread 184] INFO nextflow.processor.TaskProcessor - [86/6a2f39] Cached process > NFCORE_NANOSEQ:NANOSEQ:PREPARE_GENOME:GET_CHROM_SIZES (genome.fa) May-28 00:00:06.983 [Actor Thread 179] INFO nextflow.processor.TaskProcessor - [9d/c9c8ba] Cached process > NFCORE_NANOSEQ:NANOSEQ:PREPARE_GENOME:SAMTOOLS_FAIDX (genome.fa) May-28 00:00:06.985 [Actor Thread 179] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_NANOSEQ:NANOSEQ:PREPARE_GENOME:SAMTOOLS_FAIDX > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> May-28 00:00:07.053 [Actor Thread 193] DEBUG nextflow.container.SingularityCache - Apptainer found local store for image=docker://quay.io/biocontainers/minimap2:2.17--hed695b0_3; path=/storage/sahuarea/samuele_cancellieri/apptainer_cache/quay.io-biocontainers-minimap2-2.17--hed695b0_3.img May-28 00:00:07.069 [Actor Thread 188] INFO nextflow.processor.TaskProcessor - [75/f9984a] Cached process > NFCORE_NANOSEQ:NANOSEQ:ALIGN_MINIMAP2:MINIMAP2_INDEX (genome.fa) May-28 00:00:07.091 [Actor Thread 186] INFO nextflow.processor.TaskProcessor - [be/4be8bb] Cached process > NFCORE_NANOSEQ:NANOSEQ:ALIGN_MINIMAP2:MINIMAP2_ALIGN (WT_R1) May-28 00:00:07.098 [Actor Thread 187] DEBUG nextflow.container.SingularityCache - Apptainer found local store for image=docker://quay.io/biocontainers/samtools:1.15.1--h1170115_0; path=/storage/sahuarea/samuele_cancellieri/apptainer_cache/quay.io-biocontainers-samtools-1.15.1--h1170115_0.img May-28 00:00:07.101 [Actor Thread 188] INFO nextflow.processor.TaskProcessor - [d8/a4a7dc] Cached process > NFCORE_NANOSEQ:NANOSEQ:BAM_SORT_INDEX_SAMTOOLS:SAMTOOLS_VIEW_BAM (WT_R1) May-28 00:00:07.110 [Actor Thread 124] INFO nextflow.processor.TaskProcessor - [04/4c0195] Cached process > NFCORE_NANOSEQ:NANOSEQ:BAM_SORT_INDEX_SAMTOOLS:SAMTOOLS_SORT_INDEX (WT_R1) May-28 00:00:07.111 [Actor Thread 124] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_NANOSEQ:NANOSEQ:BAM_SORT_INDEX_SAMTOOLS:SAMTOOLS_SORT_INDEX > Skipping output binding because one or more optional files are missing: fileoutparam<1:2> May-28 00:00:07.117 [Actor Thread 191] DEBUG nextflow.container.SingularityCache - Apptainer found local store for image=docker://quay.io/biocontainers/sniffles:1.0.12--h8b12597_1; path=/storage/sahuarea/samuele_cancellieri/apptainer_cache/quay.io-biocontainers-sniffles-1.0.12--h8b12597_1.img May-28 00:00:07.117 [Actor Thread 185] DEBUG nextflow.container.SingularityCache - Apptainer found local store for image=docker://quay.io/biocontainers/bedtools:2.29.2--hc088bd4_0; path=/storage/sahuarea/samuele_cancellieri/apptainer_cache/quay.io-biocontainers-bedtools-2.29.2--hc088bd4_0.img May-28 00:00:07.120 [Actor Thread 162] INFO nextflow.processor.TaskProcessor - [49/c62079] Cached process > NFCORE_NANOSEQ:NANOSEQ:BAM_SORT_INDEX_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (WT_R1) May-28 00:00:07.122 [Actor Thread 180] INFO nextflow.processor.TaskProcessor - [fa/863f73] Cached process > NFCORE_NANOSEQ:NANOSEQ:STRUCTURAL_VARIANT_CALLING:SNIFFLES (WT_R1) May-28 00:00:07.122 [Actor Thread 189] INFO nextflow.processor.TaskProcessor - [07/3587b7] Cached process > NFCORE_NANOSEQ:NANOSEQ:BAM_SORT_INDEX_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (WT_R1) May-28 00:00:07.126 [Actor Thread 190] INFO nextflow.processor.TaskProcessor - [7d/bc47e5] Cached process > NFCORE_NANOSEQ:NANOSEQ:BEDTOOLS_UCSC_BIGWIG:BEDTOOLS_GENOMECOV (WT_R1) May-28 00:00:07.128 [Actor Thread 179] DEBUG nextflow.container.SingularityCache - Apptainer found local store for image=docker://quay.io/biocontainers/bcftools:1.20--h8b25389_0; path=/storage/sahuarea/samuele_cancellieri/apptainer_cache/quay.io-biocontainers-bcftools-1.20--h8b25389_0.img May-28 00:00:07.130 [Actor Thread 182] DEBUG nextflow.container.SingularityCache - Apptainer found local store for image=docker://quay.io/biocontainers/ucsc-bedgraphtobigwig:377--h446ed27_1; path=/storage/sahuarea/samuele_cancellieri/apptainer_cache/quay.io-biocontainers-ucsc-bedgraphtobigwig-377--h446ed27_1.img May-28 00:00:07.133 [Actor Thread 124] INFO nextflow.processor.TaskProcessor - [5f/e13d91] Cached process > NFCORE_NANOSEQ:NANOSEQ:BEDTOOLS_UCSC_BIGWIG:UCSC_BEDGRAPHTOBIGWIG (WT_R1) May-28 00:00:07.179 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run May-28 00:00:07.181 [Task submitter] INFO nextflow.Session - [ae/bba5d2] Submitted process > NFCORE_NANOSEQ:NANOSEQ:STRUCTURAL_VARIANT_CALLING:SNIFFLES_SORT_VCF (WT_R1) May-28 00:00:07.225 [Actor Thread 162] INFO nextflow.container.SingularityCache - Pulling Apptainer image docker://quay.io/biocontainers/medaka:1.4.4--py38h130def0_0 [cache /storage/sahuarea/samuele_cancellieri/apptainer_cache/quay.io-biocontainers-medaka-1.4.4--py38h130def0_0.img] May-28 00:00:07.229 [Actor Thread 192] INFO nextflow.processor.TaskProcessor - [cd/d01543] Cached process > NFCORE_NANOSEQ:NANOSEQ:BAM_SORT_INDEX_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (WT_R1) May-28 00:00:07.500 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 17; name: NFCORE_NANOSEQ:NANOSEQ:STRUCTURAL_VARIANT_CALLING:SNIFFLES_SORT_VCF (WT_R1); status: COMPLETED; exit: 255; error: -; workDir: /storage/sahuarea/samuele_cancellieri/fei_nanopore/fei_second_run/ae/bba5d24187f36ee3594c3254f39ba1] May-28 00:00:07.501 [Task monitor] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'TaskFinalizer' minSize=10; maxSize=576; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false May-28 00:00:07.506 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_NANOSEQ:NANOSEQ:STRUCTURAL_VARIANT_CALLING:SNIFFLES_SORT_VCF (WT_R1); work-dir=/storage/sahuarea/samuele_cancellieri/fei_nanopore/fei_second_run/ae/bba5d24187f36ee3594c3254f39ba1 error [nextflow.exception.ProcessFailedException]: Process `NFCORE_NANOSEQ:NANOSEQ:STRUCTURAL_VARIANT_CALLING:SNIFFLES_SORT_VCF (WT_R1)` terminated with an error exit status (255) May-28 00:00:07.518 [TaskFinalizer-1] ERROR nextflow.processor.TaskProcessor - Error executing process > 'NFCORE_NANOSEQ:NANOSEQ:STRUCTURAL_VARIANT_CALLING:SNIFFLES_SORT_VCF (WT_R1)' Caused by: Process `NFCORE_NANOSEQ:NANOSEQ:STRUCTURAL_VARIANT_CALLING:SNIFFLES_SORT_VCF (WT_R1)` terminated with an error exit status (255) Command executed: bcftools \ sort \ --temp-dir /storage/sahuarea/samuele_cancellieri/general_tmp/ \ --output WT_R1.vcf.gz \ WT_R1_sniffles.vcf cat <<-END_VERSIONS > versions.yml "NFCORE_NANOSEQ:NANOSEQ:STRUCTURAL_VARIANT_CALLING:SNIFFLES_SORT_VCF": bcftools: $(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*$//') END_VERSIONS Command exit status: 255 Command output: (empty) Command error: mkdtemp(/storage/sahuarea/samuele_cancellieri/general_tmp/8BBQ7N) failed: No such file or directory Work dir: /storage/sahuarea/samuele_cancellieri/fei_nanopore/fei_second_run/ae/bba5d24187f36ee3594c3254f39ba1 Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line May-28 00:00:07.526 [TaskFinalizer-1] INFO nextflow.Session - Execution cancelled -- Finishing pending tasks before exit May-28 00:00:07.528 [main] DEBUG nextflow.Session - Session await > all processes finished May-28 00:00:07.528 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local) - terminating tasks monitor poll loop May-28 00:00:07.528 [main] DEBUG nextflow.Session - Session await > all barriers passed May-28 00:00:07.529 [Actor Thread 186] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_NANOSEQ:NANOSEQ:SHORT_VARIANT_CALLING:MEDAKA_VARIANT; work-dir=null error [java.lang.InterruptedException]: java.lang.InterruptedException May-28 00:00:07.532 [Actor Thread 191] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 5; slices: 1; internal sort time: 0.002 s; external sort time: 0.001 s; total time: 0.003 s May-28 00:00:07.532 [Actor Thread 191] DEBUG nextflow.file.FileCollector - >> temp file exists? true May-28 00:00:07.533 [Actor Thread 191] DEBUG nextflow.file.FileCollector - Retrieved cached collect-files from: /storage/sahuarea/samuele_cancellieri/fei_nanopore/fei_second_run/collect-file/3591f445d2b1f579c2290743c3a289a5 May-28 00:00:07.535 [Actor Thread 191] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /storage/sahuarea/samuele_cancellieri/general_tmp/nxf-6154339491301595884 May-28 00:00:07.538 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'TaskFinalizer' shutdown completed (hard=false) May-28 00:00:07.538 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'PublishDir' shutdown completed (hard=false) May-28 00:00:07.540 [main] INFO nextflow.Nextflow - -[nf-core/nanoseq] Pipeline completed with errors- May-28 00:00:07.543 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=0; failedCount=1; ignoredCount=0; cachedCount=15; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=0ms; failedDuration=216ms; cachedDuration=41m 5s;loadCpus=0; loadMemory=0; peakRunning=1; peakCpus=1; peakMemory=42 GB; ] May-28 00:00:07.543 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file May-28 00:00:07.544 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report May-28 00:00:07.875 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline May-28 00:00:08.143 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done May-28 00:00:08.170 [main] INFO org.pf4j.AbstractPluginManager - Stop plugin 'nf-amazon@2.5.2' May-28 00:00:08.170 [main] DEBUG nextflow.plugin.BasePlugin - Plugin stopped nf-amazon May-28 00:00:08.171 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'FileTransfer' shutdown completed (hard=false) May-28 00:00:08.172 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye