---------------------------------------------------- ,--./,-. ___ __ __ __ ___ /,-._.--~\ |\ | |__ __ / ` / \ |__) |__ } { | \| | \__, \__/ | \ |___ \`-._,-`-, `._,._,' nf-core/mag v1.2.0 ---------------------------------------------------- Run Name: small_swartz #################################################### ## nf-core/mag execution completed unsuccessfully! ## #################################################### The exit status of the task that caused the workflow execution to fail was: 1. The full error message was: Error executing process > 'cat (SPAdes-CSJP002A-CAT_prepare_20210107)' Caused by: Process `cat (SPAdes-CSJP002A-CAT_prepare_20210107)` terminated with an error exit status (1) Command executed: CAT bins -b "bins/" -d database/ -t taxonomy/ -n "8" -s .fa --top 6 -o "SPAdes-CSJP002A" --I_know_what_Im_doing CAT add_names -i "SPAdes-CSJP002A.ORF2LCA.txt" -o "SPAdes-CSJP002A.ORF2LCA.names.txt" -t taxonomy/ CAT add_names -i "SPAdes-CSJP002A.bin2classification.txt" -o "SPAdes-CSJP002A.bin2classification.names.txt" -t taxonomy/ Command exit status: 1 Command output: # CAT v4.6. BAT is running. Protein prediction, alignment, and bin classification are carried out. Rarw! Supplied command: /opt/conda/envs/nf-core-mag-1.2.0/bin/CAT bins -b bins/ -d database/ -t taxonomy/ -n 8 -s .fa --top 6 -o SPAdes-CSJP002A --I_know_what_Im_doing Bin folder: bins/ Taxonomy folder: taxonomy/ Database folder: database/ Parameter r: 5 Parameter f: 0.3 Log file: SPAdes-CSJP002A.log ----------------- Doing some pre-flight checks first. [2021-05-07 14:21:44.515932] Prodigal found: Prodigal V2.6.3: February, 2016. [2021-05-07 14:21:44.595226] DIAMOND found: diamond version 0.9.24. [2021-05-07 14:21:44.603444] WARNING: [--top] is set lower than 50. This might conflict with future runs with higher settings of the [-r / --range] parameter, see README.md. Ready to fly! ----------------- [2021-05-07 14:21:44.609166] Importing bins from bins/. [2021-05-07 14:21:46.114194] 47 bin(s) found! [2021-05-07 14:21:46.116638] Writing SPAdes-CSJP002A.concatenated.fasta. [2021-05-07 14:21:47.942493] Running Prodigal for ORF prediction. Files SPAdes-CSJP002A.concatenated.predicted_proteins.faa and SPAdes-CSJP002A.concatenated.predicted_proteins.gff will be generated. Do not forget to cite Prodigal when using CAT or BAT in your publication! [2021-05-07 14:34:46.746849] ORF prediction done! [2021-05-07 14:34:46.756122] Parsing ORF file SPAdes-CSJP002A.concatenated.predicted_proteins.faa [2021-05-07 14:34:47.264201] Homology search with DIAMOND is starting. Please be patient. Do not forget to cite DIAMOND when using CAT or BAT in your publication! query: SPAdes-CSJP002A.concatenated.predicted_proteins.faa database: database/2021-01-07.nr.dmnd mode: fast number of cores: 8 block-size (billions of letters): 2.0 index-chunks: 4 tmpdir: ./ top: 6.0 Command error: Error: Database was built with a different version of Diamond and is incompatible. [2021-05-07 14:34:47.300571] ERROR: DIAMOND finished abnormally. Work dir: /ifs/groups/eces450650Grp/data/Assembly_Binning_old/work/81/95fee99d939f76a9ae31784c62007d Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run` The workflow was completed at 2021-05-07T14:47:11.875034-04:00 (duration: 1h 4m 7s) The command used to launch the workflow was as follows: nextflow run nf-core/mag -resume -profile singularity --input 'CSJP002A_{R1,R2}.fastq.gz' -c nextflow.config --max_memory 186.GB --max_cpus 20 --kraken2_db k2_pluspf_20210127.tar.gz --cat_db CAT_prepare_20210107.tar.gz --outdir results_cat Pipeline Configuration: ----------------------- - Pipeline Release: master - Run Name: small_swartz - Input: CSJP002A_{R1,R2}.fastq.gz - Data Type: Paired-End - Adapter forward: AGATCGGAAGAGCACACGTCTGAACTCCAGTCA - Adapter reverse: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT - Mean quality: 15 - Trimming quality: 15 - Keep phix reads: No - PhiX reference: /home/gailr/.nextflow/assets/nf-core/mag/assets/data/GCA_002596845.1_ASM259684v1_genomic.fna.gz - Kraken2 Db: k2_pluspf_20210127.tar.gz - Skip_krona: No - Skip binning: No - Binning mapping mode: group - Min contig size: 1500 - Min length unbinned contigs: 1000000 - Max unbinned contigs: 100 - Skip busco: No - Busco Reference: https://busco-data.ezlab.org/v4/data/lineages/bacteria_odb10.2020-03-06.tar.gz - Co-assemble group: No - Skip spades: No - Skip spadeshybrid: No - Skip megahit: No - Skip quast: No - MEGAHIT fix cpus: No - SPAdes fix cpus: No - MetaBAT2 RNG seed: 1 - Max Resources: 186.GB memory, 20 cpus, 10d time per job - Container: singularity - nfcore/mag:1.2.0 - Output dir: results_cat - Launch dir: /ifs/groups/eces450650Grp/data/Assembly_Binning_old - Working dir: /ifs/groups/eces450650Grp/data/Assembly_Binning_old/work - Script dir: /home/gailr/.nextflow/assets/nf-core/mag - User: gailr - Config Profile: singularity - Config Files: /home/gailr/.nextflow/config, /home/gailr/.nextflow/assets/nf-core/mag/nextflow.config, /ifs/groups/eces450650Grp/data/Assembly_Binning_old/nextflow.config, /ifs/groups/eces450650Grp/data/Assembly_Binning_old/nextflow.config - Date Started: 2021-05-07T13:43:04.718919-04:00 - Date Completed: 2021-05-07T14:47:11.875034-04:00 - Pipeline script file path: /home/gailr/.nextflow/assets/nf-core/mag/main.nf - Pipeline script hash ID: 9cb2acf745c45b148cca2622d7dccaa8 - Pipeline repository Git URL: https://github.com/nf-core/mag - Pipeline repository Git Commit: 485c3fa0ba7345ac124bef04d08391d5e7cdcb42 - Pipeline Git branch/tag: master - Nextflow Version: 20.10.0 - Nextflow Build: 5430 - Nextflow Compile Timestamp: 01-11-2020 15:14 UTC -- nf-core/mag https://github.com/nf-core/mag