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Published 20 hours ago • verified publisher icon nf-core

Error in TABULAR_TO_GSEA_CHIP

Open acpicornell opened this issue 10 months ago • 1 comments

Description of the bug

Hello,

I am trying to run GSEA but I get an error when trying to process the GMT file I obtained from MSigDB.

Previously, I have executed the pipeline without the GSEA part, and the differential expression analysis works without any issues.

Is anyone else encountering this problem?

Thank you very much.

Command used and terminal output

#!/bin/bash

#SBATCH --nodes=1
#SBATCH --partition bioinfo
#SBATCH --output=rnaseq_de_%j.out
#SBATCH --error=rnaseq_de_%j.err
#SBATCH --mail-type=END,FAIL

export NXF_EXECUTOR=slurm

#Parameters
date="240405"
scratch_dir="/mnt/storage/scratch/hgugm_"$SLURM_JOB_ID
analysis_dir="/mnt/storage/user1/thytreg/"$date

echo "Use Java downloaded by SDKMAN"
export JAVA_HOME="/home/user1/.sdkman/candidates/java/17.0.6-amzn"

echo "Automatic downloads and updates are enabled."
export NXF_OFFLINE=false

echo "Use NEXTFLOW version 23.10.1"
export NXF_VER=23.10.1

echo "Define workdir in /scratch:"
echo ${scratch_dir}
mkdir -p ${scratch_dir}
export NXF_WORK=${scratch_dir}

echo "Differential expression EXEC:"
srun /mnt/storage/$(whoami)/bin/nextflow run /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0\
     --study_type      		rnaseq\
     --input            	/mnt/storage/$(whoami)/thytreg/${date}/samplesheet.csv\
     --outdir           	/mnt/storage/$(whoami)/thytreg/${date}/output\
     --matrix           	/mnt/storage/$(whoami)/thytreg/${date}/salmon.merged.gene_counts.tsv\
     --transcript_length_matrix /mnt/storage/$(whoami)/thytreg/${date}/salmon.merged.gene_lengths.tsv\
     --contrasts		/mnt/storage/$(whoami)/thytreg/${date}/contrasts.csv\
     --gtf			/mnt/storage/data/ncbi/data/GCF_000001405.40/genomic.gtf\
     --features_id_col          gene_id\
     --features_name_col        gene_name\
     --features_type 		gene\
     --gsea_run			TRUE\
     --gsea_gene_sets           /mnt/storage/data/gsea/c2.cp.v2023.2.Hs.symbols.gmt\
     -profile                   rnaseq,singularity\
     -c                 	/home/$(whoami)/configs/nextflow_slurm.config\

And I get:

executor >  slurm (7)
[63/ef6582] process > NFCORE_DIFFERENTIALABUNDANC... [100%] 1 of 1 ✔
[58/750c31] process > NFCORE_DIFFERENTIALABUNDANC... [100%] 1 of 1 ✔
[c3/7880b1] process > NFCORE_DIFFERENTIALABUNDANC... [  0%] 0 of 1
[-        ] process > NFCORE_DIFFERENTIALABUNDANC... -
[-        ] process > NFCORE_DIFFERENTIALABUNDANC... -
[-        ] process > NFCORE_DIFFERENTIALABUNDANC... -
[21/0db74c] process > NFCORE_DIFFERENTIALABUNDANC... [  0%] 0 of 3
[bb/9d07fb] process > NFCORE_DIFFERENTIALABUNDANC... [  0%] 0 of 1
[-        ] process > NFCORE_DIFFERENTIALABUNDANC... -
[-        ] process > NFCORE_DIFFERENTIALABUNDANC... -
[-        ] process > NFCORE_DIFFERENTIALABUNDANC... -
[-        ] process > NFCORE_DIFFERENTIALABUNDANC... -
[-        ] process > NFCORE_DIFFERENTIALABUNDANC... -
[-        ] process > NFCORE_DIFFERENTIALABUNDANC... -
[-        ] process > NFCORE_DIFFERENTIALABUNDANC... -
ERROR ~ Error executing process > 'NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:TABULAR_TO_GSEA_CHIP (1)'

Caused by:
  Process `NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:TABULAR_TO_GSEA_CHIP (1)` terminated with an error exit status (1)

Command executed:

  function find_column_number {
      file=$1
      column=$2
  
      head -n 1 $file | tr '\t' '\n' | grep -n "^${column}$" | awk -F':' '{print $1}'
  }
  
  id_col=$(find_column_number genomic.anno.feature_metadata.tsv gene_id)
  symbol_col=$(find_column_number genomic.anno.feature_metadata.tsv gene_name)
  outfile=$(echo genomic.anno.feature_metadata.tsv | sed 's/\(.*\)\..*/\1/').chip
  
  echo -e "Probe Set ID\tGene Symbol\tGene Title" > ${outfile}.tmp
  tail -n +2 genomic.anno.feature_metadata.tsv | awk -F'\t' -v id=$id_col -v symbol=$symbol_col '{print $id"\t"$symbol"\tNA"}' >> ${outfile}.tmp
  mv ${outfile}.tmp ${outfile}
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:TABULAR_TO_GSEA_CHIP":
      bash: $(echo $(bash --version | grep -Eo 'version [[:alnum:].]+' | sed 's/version //'))
  END_VERSIONS

Command exit status:
  1

Relevant files

Apr-09 13:16:47.240 [main] DEBUG nextflow.cli.Launcher - $> nextflow run /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0 --study_type rnaseq --input /mnt/storage/acpicornell/thytreg/240405/samplesheet.csv --outdir /mnt/storage/acpicornell/thytreg/240405/output --matrix /mnt/storage/acpicornell/thytreg/240405/salmon.merged.gene_counts.tsv --transcript_length_matrix /mnt/storage/acpicornell/thytreg/240405/salmon.merged.gene_lengths.tsv --contrasts /mnt/storage/acpicornell/thytreg/240405/contrasts.csv --gtf /mnt/storage/data/ncbi/data/GCF_000001405.40/genomic.gtf --features_id_col gene_id --features_name_col gene_name --features_type gene --gsea_run TRUE --gsea_gene_sets /mnt/storage/data/gsea/c2.cp.v2023.2.Hs.symbols.gmt -profile rnaseq,singularity -c /home/acpicornell/configs/nextflow_slurm.config Apr-09 13:16:47.359 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 23.10.1 Apr-09 13:16:47.378 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/user1/.nextflow/plugins; core-plugins: [email protected],[email protected],[email protected],[email protected],[email protected],[email protected],[email protected],[email protected],[email protected] Apr-09 13:16:47.387 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: [] Apr-09 13:16:47.388 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: [] Apr-09 13:16:47.391 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode Apr-09 13:16:47.408 [main] INFO org.pf4j.AbstractPluginManager - No plugins Apr-09 13:16:49.107 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/nextflow.config Apr-09 13:16:49.110 [main] DEBUG nextflow.config.ConfigBuilder - User config file: /home/user1/configs/nextflow_slurm.config Apr-09 13:16:49.111 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/nextflow.config Apr-09 13:16:49.111 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/user1/configs/nextflow_slurm.config Apr-09 13:16:49.132 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: rnaseq,singularity Apr-09 13:16:51.513 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: rnaseq,singularity Apr-09 13:16:51.580 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [cfc_dev, uzl_omics, ifb_core, denbi_qbic, alice, mjolnir_globe, uppmax, incliva, ilifu, uge, rosalind_uge, lugh, unibe_ibu, vai, soft, test_soft, czbiohub_aws, jax, ccga_med, scw, unc_longleaf, tigem, tubingen_apg, google, apollo, ipop_up, vsc_calcua, pdc_kth, googlels, daisybio, eddie, medair, biowulf, test_maxquant, apptainer, bi, bigpurple, adcra, cedars, pawsey_setonix, vsc_kul_uhasselt, pawsey_nimbus, ucl_myriad, utd_ganymede, charliecloud, icr_davros, ceres, munin, arm, rosalind, rnaseq, 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, affy, mpcdf, leicester, vsc_ugent, create, sage, cambridge, jex, podman, ebi_codon, cheaha, xanadu, nyu_hpc, test, computerome, ucd_sonic, seg_globe, sanger, dkfz, pasteur, ethz_euler, m3c, test_full, imb, ucl_cscluster, tuos_stanage, azurebatch, hki, crukmi, csiro_petrichor, qmul_apocrita, docker, engaging, gis, hypatia, psmn, eva, nygc, test_nogtf, fgcz, conda, crg, singularity, self_hosted_runner, tufts, uw_hyak_pedslabs, utd_sysbio, debug, test_affy, genouest, cbe, phoenix, gitpod, seawulf, uod_hpc, fub_curta, uct_hpc, aws_tower, binac] Apr-09 13:16:51.644 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declararion Apr-09 13:16:51.665 [main] INFO nextflow.cli.CmdRun - Launching /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/main.nf [prickly_neumann] DSL2 - revision: 2a636b2a04 Apr-09 13:16:51.666 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins declared=[nf-validation] Apr-09 13:16:51.667 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[] Apr-09 13:16:51.667 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[nf-validation] Apr-09 13:16:51.667 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-validation version: latest Apr-09 13:16:52.415 [main] INFO org.pf4j.AbstractPluginManager - Plugin '[email protected]' resolved Apr-09 13:16:52.416 [main] INFO org.pf4j.AbstractPluginManager - Start plugin '[email protected]' Apr-09 13:16:52.422 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started [email protected] Apr-09 13:16:52.433 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /home/user1/.nextflow/secrets/store.json Apr-09 13:16:52.436 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@79b8ecb] - activable => nextflow.secret.LocalSecretsProvider@79b8ecb Apr-09 13:16:52.502 [main] DEBUG nextflow.Session - Session UUID: 1c2cadfc-259f-4005-bf34-c1f7b1a9e852 Apr-09 13:16:52.503 [main] DEBUG nextflow.Session - Run name: prickly_neumann Apr-09 13:16:52.503 [main] DEBUG nextflow.Session - Executor pool size: 2 Apr-09 13:16:52.512 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null Apr-09 13:16:52.517 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=10; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false Apr-09 13:16:52.540 [main] DEBUG nextflow.cli.CmdRun - Version: 23.10.1 build 5891 Created: 12-01-2024 22:01 UTC (23:01 CEST) System: Linux 5.14.0-362.24.1.el9_3.x86_64 Runtime: Groovy 3.0.19 on OpenJDK 64-Bit Server VM 17.0.6+10-LTS Encoding: UTF-8 (UTF-8) Process: [email protected] [192.168.224.6] CPUs: 2 - Mem: 125 GB (23 GB) - Swap: 4 GB (3.6 GB) Apr-09 13:16:52.564 [main] DEBUG nextflow.Session - Work-dir: /mnt/storage/scratch/hgugm_93947 [xfs] Apr-09 13:16:52.580 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[] Apr-09 13:16:52.590 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory Apr-09 13:16:52.694 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory Apr-09 13:16:52.705 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 3; maxThreads: 1000 Apr-09 13:16:52.889 [main] DEBUG nextflow.Session - Session start Apr-09 13:16:52.895 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /mnt/storage/user1/thytreg/240405/output/pipeline_info/execution_trace_2024-04-09_13-16-50.txt Apr-09 13:16:52.909 [main] DEBUG nextflow.Session - Using default localLib path: /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/lib Apr-09 13:16:52.912 [main] DEBUG nextflow.Session - Adding to the classpath library: /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/lib Apr-09 13:16:52.912 [main] DEBUG nextflow.Session - Adding to the classpath library: /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/lib/nfcore_external_java_deps.jar Apr-09 13:16:53.672 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution Apr-09 13:16:53.686 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [validateParameters:validateParameters, paramsHelp:paramsHelp]; plugin Id: nf-validation Apr-09 13:16:53.703 [main] DEBUG nextflow.validation.SchemaValidator - Starting parameters validation Apr-09 13:16:54.023 [main] DEBUG nextflow.validation.SchemaValidator - Starting validation: 'input': '/mnt/storage/user1/thytreg/240405/samplesheet.csv' with '/mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/assets/schema_input.json' Apr-09 13:16:54.050 [main] DEBUG nextflow.validation.SchemaValidator - Validation passed: 'input': '/mnt/storage/user1/thytreg/240405/samplesheet.csv' with '/mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/assets/schema_input.json' Apr-09 13:16:54.052 [main] DEBUG nextflow.validation.SchemaValidator - Finishing parameters validation Apr-09 13:16:55.333 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryLog:paramsSummaryLog, paramsSummaryMap:paramsSummaryMap]; plugin Id: nf-validation Apr-09 13:16:55.358 [main] INFO nextflow.Nextflow -

                                    ,--./,-.
    ___     __   __   __   ___     /,-._.--~'

|\ | |__ __ / / \ |__) |__ } { | \| | \__, \__/ | \ |___ \-.,--, .,._,' nf-core/differentialabundance v1.4.0

Core Nextflow options runName : prickly_neumann containerEngine : singularity container : [RMARKDOWNNOTEBOOK:biocontainers/r-shinyngs:1.8.4--r43hdfd78af_0] launchDir : /mnt/storage/user1/thytreg/240405 workDir : /mnt/storage/scratch/hgugm_93947 projectDir : /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0 userName : user1 profile : rnaseq,singularity configFiles :

Input/output options input : /mnt/storage/user1/thytreg/240405/samplesheet.csv contrasts : /mnt/storage/user1/thytreg/240405/contrasts.csv outdir : /mnt/storage/user1/thytreg/240405/output

Abundance values matrix : /mnt/storage/user1/thytreg/240405/salmon.merged.gene_counts.tsv transcript_length_matrix : /mnt/storage/user1/thytreg/240405/salmon.merged.gene_lengths.tsv affy_cel_files_archive : null querygse : null

Affy input options affy_cdfname : null

Proteus input options proteus_round_digits : -1

Filtering filtering_min_abundance : 1 filtering_min_samples : 1

Differential analysis differential_min_fold_change: 2 differential_max_pval : 1

Limma specific options (microarray only) limma_spacing : null limma_block : null limma_correlation : null limma_p_value : 1

GSEA gsea_run : true gsea_gene_sets : /mnt/storage/data/gsea/c2.cp.v2023.2.Hs.symbols.gmt

Shiny app settings shinyngs_shinyapps_account : null shinyngs_shinyapps_app_name : null

Reporting options report_file : /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/assets/differentialabundance_report.Rmd logo_file : /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/docs/images/nf-core-differentialabundance_logo_light.png css_file : /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/assets/nf-core_style.css citations_file : /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/CITATIONS.md report_title : null report_author : null report_description : null

Reference genome options gtf : /mnt/storage/data/ncbi/data/GCF_000001405.40/genomic.gtf

Institutional config options custom_config_base : /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/../configs/ config_profile_name : RNA-seq profile config_profile_description : IiSGM SLURM profile in single nodes

Max job request options max_cpus : 32 max_memory : 100 GB max_time : 5d

!! Only displaying parameters that differ from the pipeline defaults !!

If you use nf-core/differentialabundance for your analysis please cite:

  • The pipeline https://doi.org/10.5281/zenodo.7568000

  • The nf-core framework https://doi.org/10.1038/s41587-020-0439-x

  • Software dependencies https://github.com/nf-core/differentialabundance/blob/master/CITATIONS.md

Apr-09 13:16:58.334 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_single matches labels process_single for process with name NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:GTF_TO_TABLE Apr-09 13:16:58.337 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:GTF_TO_TABLE matches process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:GTF_TO_TABLE Apr-09 13:16:58.349 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-09 13:16:58.349 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-09 13:16:58.358 [main] DEBUG nextflow.executor.Executor - [warm up] executor > slurm Apr-09 13:16:58.362 [main] DEBUG n.processor.TaskPollingMonitor - Creating task monitor for executor 'slurm' > capacity: 50; pollInterval: 15s; dumpInterval: 5m Apr-09 13:16:58.364 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: slurm) Apr-09 13:16:58.366 [main] DEBUG n.executor.AbstractGridExecutor - Creating executor 'slurm' > queue-stat-interval: 1m Apr-09 13:16:58.499 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_single matches labels process_single for process with name NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:VALIDATOR Apr-09 13:16:58.500 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:VALIDATOR matches process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:VALIDATOR Apr-09 13:16:58.504 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-09 13:16:58.504 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-09 13:16:58.523 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_single matches labels process_single for process with name NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_MATRIXFILTER Apr-09 13:16:58.524 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:CUSTOM_MATRIXFILTER matches process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_MATRIXFILTER Apr-09 13:16:58.527 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-09 13:16:58.527 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-09 13:16:58.546 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_medium matches labels process_medium for process with name NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:DESEQ2_NORM Apr-09 13:16:58.547 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:DESEQ2_DIFFERENTIAL matches process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:DESEQ2_NORM Apr-09 13:16:58.547 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:DESEQ2_NORM matches process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:DESEQ2_NORM Apr-09 13:16:58.553 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-09 13:16:58.553 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-09 13:16:58.566 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_medium matches labels process_medium for process with name NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:DESEQ2_DIFFERENTIAL Apr-09 13:16:58.566 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:DESEQ2_DIFFERENTIAL matches process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:DESEQ2_DIFFERENTIAL Apr-09 13:16:58.570 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-09 13:16:58.570 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-09 13:16:58.587 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_single matches labels process_single for process with name NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_TABULARTOGSEAGCT Apr-09 13:16:58.590 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:CUSTOM_TABULARTOGSEAGCT matches process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_TABULARTOGSEAGCT Apr-09 13:16:58.606 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-09 13:16:58.608 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-09 13:16:58.628 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_single matches labels process_single for process with name NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_TABULARTOGSEACLS Apr-09 13:16:58.628 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:CUSTOM_TABULARTOGSEACLS matches process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_TABULARTOGSEACLS Apr-09 13:16:58.633 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-09 13:16:58.633 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-09 13:16:58.638 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_single matches labels process_single for process with name NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:TABULAR_TO_GSEA_CHIP Apr-09 13:16:58.639 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:TABULAR_TO_GSEA_CHIP matches process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:TABULAR_TO_GSEA_CHIP Apr-09 13:16:58.640 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-09 13:16:58.640 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-09 13:16:58.658 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_single matches labels process_single for process with name NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:GSEA_GSEA Apr-09 13:16:58.659 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:GSEA_GSEA matches process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:GSEA_GSEA Apr-09 13:16:58.661 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-09 13:16:58.661 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-09 13:16:58.694 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_single matches labels process_single for process with name NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_EXPLORATORY Apr-09 13:16:58.695 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:PLOT_EXPLORATORY matches process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_EXPLORATORY Apr-09 13:16:58.697 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-09 13:16:58.697 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-09 13:16:58.704 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_single matches labels process_single for process with name NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_DIFFERENTIAL Apr-09 13:16:58.705 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:PLOT_DIFFERENTIAL matches process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_DIFFERENTIAL Apr-09 13:16:58.707 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-09 13:16:58.707 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-09 13:16:58.728 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_single matches labels process_single for process with name NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_DUMPSOFTWAREVERSIONS Apr-09 13:16:58.728 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:CUSTOM_DUMPSOFTWAREVERSIONS matches process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_DUMPSOFTWAREVERSIONS Apr-09 13:16:58.729 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-09 13:16:58.729 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-09 13:16:58.784 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_single matches labels process_single for process with name NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:SHINYNGS_APP Apr-09 13:16:58.785 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:SHINYNGS_APP matches process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:SHINYNGS_APP Apr-09 13:16:58.786 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-09 13:16:58.786 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-09 13:16:58.797 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_low matches labels process_low for process with name NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:RMARKDOWNNOTEBOOK Apr-09 13:16:58.798 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:RMARKDOWNNOTEBOOK matches process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:RMARKDOWNNOTEBOOK Apr-09 13:16:58.799 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-09 13:16:58.799 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-09 13:16:58.808 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_single matches labels process_single for process with name NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:MAKE_REPORT_BUNDLE Apr-09 13:16:58.809 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:MAKE_REPORT_BUNDLE matches process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:MAKE_REPORT_BUNDLE Apr-09 13:16:58.809 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Apr-09 13:16:58.809 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Apr-09 13:16:58.812 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: VALIDATOR, ZIP, NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_MATRIXFILTER, CUSTOM_TABULARTOGSEAGCT, MAKE_REPORT_BUNDLE, ATLASGENEANNOTATIONMANIPULATION_GTF2FEATUREANNOTATION, NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:GSEA_GSEA, PLOT_DIFFERENTIAL, NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:GTF_TO_TABLE, NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:VALIDATOR, NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:DESEQ2_NORM, GSEA_GSEA, SHINYNGS_VALIDATEFOMCOMPONENTS, NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:SHINYNGS_APP, GUNZIP_GTF, AFFY_JUSTRMA, NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:TABULAR_TO_GSEA_CHIP, NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_DUMPSOFTWAREVERSIONS, TABULAR_TO_GSEA_CHIP, CUSTOM_TABULARTOGSEACLS, GUNZIP, SHINYNGS_STATICDIFFERENTIAL, UNTAR, AFFY_JUSTRMA_RAW, NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:RMARKDOWNNOTEBOOK, GTF_TO_TABLE, GEOQUERY_GETGEO, PROTEUS_READPROTEINGROUPS, NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_TABULARTOGSEAGCT, NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:MAKE_REPORT_BUNDLE, DESEQ2_DIFFERENTIAL, SHINYNGS_STATICEXPLORATORY, DESEQ2_NORM, NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:DESEQ2_DIFFERENTIAL, RMARKDOWNNOTEBOOK, LIMMA_DIFFERENTIAL, SHINYNGS_APP, CUSTOM_DUMPSOFTWAREVERSIONS, CUSTOM_MATRIXFILTER, PLOT_EXPLORATORY, NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_TABULARTOGSEACLS, PROTEUS, NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_EXPLORATORY, AFFY_JUSTRMA_NORM, NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_DIFFERENTIAL Apr-09 13:16:58.821 [main] DEBUG nextflow.Session - Igniting dataflow network (25) Apr-09 13:16:58.826 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:GTF_TO_TABLE Apr-09 13:16:58.834 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:VALIDATOR Apr-09 13:16:58.834 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_MATRIXFILTER Apr-09 13:16:58.834 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:DESEQ2_NORM Apr-09 13:16:58.834 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:DESEQ2_DIFFERENTIAL Apr-09 13:16:58.834 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_TABULARTOGSEAGCT Apr-09 13:16:58.835 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_TABULARTOGSEACLS Apr-09 13:16:58.835 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:TABULAR_TO_GSEA_CHIP Apr-09 13:16:58.835 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:GSEA_GSEA Apr-09 13:16:58.835 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_EXPLORATORY Apr-09 13:16:58.835 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_DIFFERENTIAL Apr-09 13:16:58.836 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_DUMPSOFTWAREVERSIONS Apr-09 13:16:58.840 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:SHINYNGS_APP Apr-09 13:16:58.841 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:RMARKDOWNNOTEBOOK Apr-09 13:16:58.841 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:MAKE_REPORT_BUNDLE Apr-09 13:16:58.842 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files: Script_736359fe28427d7c: /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/./workflows/../modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/main.nf Script_0b2b547b5bd8d72f: /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/./workflows/../modules/nf-core/deseq2/differential/main.nf Script_bd162165863945c5: /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/./workflows/../modules/nf-core/shinyngs/validatefomcomponents/main.nf Script_8258fa18ec202f1e: /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/./workflows/../modules/nf-core/geoquery/getgeo/main.nf Script_fd29bcfb844eda4d: /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/./workflows/../modules/nf-core/limma/differential/main.nf Script_e11ffbac6afe36ec: /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/./workflows/../modules/nf-core/gsea/gsea/main.nf Script_c3c7f0ae80cda0cc: /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/./workflows/../modules/nf-core/shinyngs/staticexploratory/main.nf Script_66ffa6df5b55d922: /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/main.nf Script_f291caf4f7573aca: /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/./workflows/../modules/nf-core/custom/tabulartogseagct/main.nf Script_af0fb319323fde68: /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/./workflows/../modules/nf-core/affy/justrma/main.nf Script_61045595cd57fdfa: /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/./workflows/../modules/nf-core/custom/tabulartogseacls/main.nf Script_cb1a92e48950cb6f: /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/./workflows/../modules/nf-core/shinyngs/app/main.nf Script_36fafb73beaa89a0: /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/./workflows/../modules/nf-core/rmarkdownnotebook/main.nf Script_a9670c657bdfaa03: /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/./workflows/../modules/local/tabular_to_gsea_chip.nf Script_1a6661f1fced92e0: /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/./workflows/../modules/nf-core/rmarkdownnotebook/./parametrize.nf Script_980ffca4de0b9bc8: /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/./workflows/../modules/nf-core/shinyngs/staticdifferential/main.nf Script_c901260d3c3d641a: /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/./workflows/../modules/nf-core/custom/matrixfilter/main.nf Script_777604ec37a36f79: /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/./workflows/../modules/nf-core/custom/dumpsoftwareversions/main.nf Script_66471300492dce16: /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/./workflows/differentialabundance.nf Script_7002cd4537b0f229: /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/./workflows/../modules/nf-core/proteus/readproteingroups/main.nf Script_079385570c0cda9d: /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/./workflows/../modules/nf-core/untar/main.nf Script_b4abc93ac1f4bba3: /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/./workflows/../modules/nf-core/zip/main.nf Script_a71c717f63173976: /mnt/storage/singularity/pipelines/nf-core-differentialabundance_1.4.0/1_4_0/./workflows/../modules/nf-core/gunzip/main.nf Apr-09 13:16:58.842 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination Apr-09 13:16:58.842 [main] DEBUG nextflow.Session - Session await Apr-09 13:16:58.905 [Actor Thread 6] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/atlas-gene-annotation-manipulation%3A1.1.0--hdfd78af_0; path=/mnt/storage/singularity/cache/depot.galaxyproject.org-singularity-atlas-gene-annotation-manipulation%3A1.1.0--hdfd78af_0.img Apr-09 13:16:59.023 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:GTF_TO_TABLE (genomic) > jobId: 93948; workDir: /mnt/storage/scratch/hgugm_93947/63/ef6582369bb192473c82f71d1aa553 Apr-09 13:16:59.023 [Task submitter] INFO nextflow.Session - [63/ef6582] Submitted process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:GTF_TO_TABLE (genomic) Apr-09 13:17:13.445 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 93948; id: 1; name: NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:GTF_TO_TABLE (genomic); status: COMPLETED; exit: 0; error: -; workDir: /mnt/storage/scratch/hgugm_93947/63/ef6582369bb192473c82f71d1aa553 started: 1712661433434; exited: 2024-04-09T11:17:13.341673264Z; ] Apr-09 13:17:13.610 [Actor Thread 1] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/r-shinyngs:1.8.4--r43hdfd78af_0; path=/mnt/storage/singularity/cache/depot.galaxyproject.org-singularity-r-shinyngs-1.8.4--r43hdfd78af_0.img Apr-09 13:17:13.625 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:GTF_TO_TABLE > Skipping output binding because one or more optional files are missing: fileoutparam<1:1> Apr-09 13:17:13.650 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:VALIDATOR (samplesheet.csv) > jobId: 93949; workDir: /mnt/storage/scratch/hgugm_93947/58/750c316aef52caf4b6414f176971a0 Apr-09 13:17:13.651 [Task submitter] INFO nextflow.Session - [58/750c31] Submitted process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:VALIDATOR (samplesheet.csv) Apr-09 13:17:13.658 [Task monitor] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'PublishDir' minSize=10; maxSize=10; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false Apr-09 13:17:43.434 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 93949; id: 2; name: NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:VALIDATOR (samplesheet.csv); status: COMPLETED; exit: 0; error: -; workDir: /mnt/storage/scratch/hgugm_93947/58/750c316aef52caf4b6414f176971a0 started: 1712661448432; exited: 2024-04-09T11:17:29.020728634Z; ] Apr-09 13:17:43.465 [Actor Thread 5] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/gawk:5.1.0; path=/mnt/storage/singularity/cache/depot.galaxyproject.org-singularity-gawk-5.1.0.img Apr-09 13:17:43.521 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:TABULAR_TO_GSEA_CHIP (1) > jobId: 93950; workDir: /mnt/storage/scratch/hgugm_93947/bb/9d07fbd8936c73b346a3b3961db1ca Apr-09 13:17:43.521 [Task submitter] INFO nextflow.Session - [bb/9d07fb] Submitted process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:TABULAR_TO_GSEA_CHIP (1) Apr-09 13:17:43.557 [Actor Thread 12] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/r-base:4.2.1; path=/mnt/storage/singularity/cache/depot.galaxyproject.org-singularity-r-base-4.2.1.img Apr-09 13:17:43.564 [Actor Thread 16] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/ubuntu:20.04; path=/mnt/storage/singularity/cache/depot.galaxyproject.org-singularity-ubuntu-20.04.img Apr-09 13:17:43.611 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_TABULARTOGSEACLS (PTREG_THY) > jobId: 93951; workDir: /mnt/storage/scratch/hgugm_93947/9f/69878e624c65d509e991b42369590f Apr-09 13:17:43.612 [Task submitter] INFO nextflow.Session - [9f/69878e] Submitted process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_TABULARTOGSEACLS (PTREG_THY) Apr-09 13:17:43.627 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_TABULARTOGSEACLS (PTREG_UCB) > jobId: 93952; workDir: /mnt/storage/scratch/hgugm_93947/a6/5e105b1fe42c43b373e3401cc10038 Apr-09 13:17:43.627 [Task submitter] INFO nextflow.Session - [a6/5e105b] Submitted process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_TABULARTOGSEACLS (PTREG_UCB) Apr-09 13:17:43.643 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_TABULARTOGSEACLS (UCB_THY) > jobId: 93953; workDir: /mnt/storage/scratch/hgugm_93947/21/0db74c4adfc8cf01b83e811c6cb162 Apr-09 13:17:43.643 [Task submitter] INFO nextflow.Session - [21/0db74c] Submitted process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_TABULARTOGSEACLS (UCB_THY) Apr-09 13:17:43.656 [Task submitter] DEBUG nextflow.executor.GridTaskHandler - [SLURM] submitted process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_MATRIXFILTER ([id:study]) > jobId: 93954; workDir: /mnt/storage/scratch/hgugm_93947/c3/7880b13be409b600288e83ecd6e5c2 Apr-09 13:17:43.656 [Task submitter] INFO nextflow.Session - [c3/7880b1] Submitted process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_MATRIXFILTER ([id:study]) Apr-09 13:17:58.440 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 93950; id: 3; name: NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:TABULAR_TO_GSEA_CHIP (1); status: COMPLETED; exit: 1; error: -; workDir: /mnt/storage/scratch/hgugm_93947/bb/9d07fbd8936c73b346a3b3961db1ca started: 1712661478434; exited: 2024-04-09T11:17:44.207782267Z; ] Apr-09 13:17:58.451 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for task: name=NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:TABULAR_TO_GSEA_CHIP (1); work-dir=/mnt/storage/scratch/hgugm_93947/bb/9d07fbd8936c73b346a3b3961db1ca error [nextflow.exception.ProcessFailedException]: Process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:TABULAR_TO_GSEA_CHIP (1) terminated with an error exit status (1) Apr-09 13:17:58.474 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:TABULAR_TO_GSEA_CHIP (1)'

Caused by: Process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:TABULAR_TO_GSEA_CHIP (1) terminated with an error exit status (1)

Command executed:

function find_column_number { file=$1 column=$2

  head -n 1 $file | tr '\t' '\n' | grep -n "^${column}$" | awk -F':' '{print $1}'

}

id_col=$(find_column_number genomic.anno.feature_metadata.tsv gene_id) symbol_col=$(find_column_number genomic.anno.feature_metadata.tsv gene_name) outfile=$(echo genomic.anno.feature_metadata.tsv | sed 's/(.)../\1/').chip

echo -e "Probe Set ID\tGene Symbol\tGene Title" > ${outfile}.tmp tail -n +2 genomic.anno.feature_metadata.tsv | awk -F'\t' -v id=$id_col -v symbol=$symbol_col '{print $id"\t"$symbol"\tNA"}' >> ${outfile}.tmp mv ${outfile}.tmp ${outfile}

cat <<-END_VERSIONS > versions.yml "NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:TABULAR_TO_GSEA_CHIP": bash: $(echo $(bash --version | grep -Eo 'version [[:alnum:].]+' | sed 's/version //')) END_VERSIONS

Command exit status: 1

Command output: (empty)

Work dir: /mnt/storage/scratch/hgugm_93947/bb/9d07fbd8936c73b346a3b3961db1ca

Tip: when you have fixed the problem you can continue the execution adding the option -resume to the run command line Apr-09 13:17:58.491 [Task monitor] INFO nextflow.Session - Execution cancelled -- Finishing pending tasks before exit Apr-09 13:17:58.494 [main] DEBUG nextflow.Session - Session await > all processes finished Apr-09 13:17:58.506 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 93951; id: 5; name: NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_TABULARTOGSEACLS (PTREG_THY); status: COMPLETED; exit: 0; error: -; workDir: /mnt/storage/scratch/hgugm_93947/9f/69878e624c65d509e991b42369590f started: 1712661478504; exited: 2024-04-09T11:17:44.326782687Z; ] Apr-09 13:17:58.519 [Actor Thread 3] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 2; slices: 1; internal sort time: 0.017 s; external sort time: 0.001 s; total time: 0.018 s Apr-09 13:17:58.525 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 93952; id: 6; name: NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_TABULARTOGSEACLS (PTREG_UCB); status: COMPLETED; exit: 0; error: -; workDir: /mnt/storage/scratch/hgugm_93947/a6/5e105b1fe42c43b373e3401cc10038 started: 1712661478525; exited: 2024-04-09T11:17:44.291782564Z; ] Apr-09 13:17:58.540 [Actor Thread 3] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /mnt/storage/scratch/hgugm_93947/collect-file/528b46773b4417d538eb709b5dafcdb3 Apr-09 13:17:58.544 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 93953; id: 7; name: NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_TABULARTOGSEACLS (UCB_THY); status: COMPLETED; exit: 0; error: -; workDir: /mnt/storage/scratch/hgugm_93947/21/0db74c4adfc8cf01b83e811c6cb162 started: 1712661478544; exited: 2024-04-09T11:17:44.291782564Z; ] Apr-09 13:17:58.552 [Actor Thread 3] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-10896104743810972899 Apr-09 13:17:58.554 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[jobId: 93954; id: 4; name: NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_MATRIXFILTER ([id:study]); status: COMPLETED; exit: 0; error: -; workDir: /mnt/storage/scratch/hgugm_93947/c3/7880b13be409b600288e83ecd6e5c2 started: 1712661478554; exited: 2024-04-09T11:17:45.329786229Z; ] Apr-09 13:17:58.574 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: slurm) - terminating tasks monitor poll loop Apr-09 13:17:58.576 [main] DEBUG nextflow.Session - Session await > all barriers passed Apr-09 13:17:58.580 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'PublishDir' shutdown completed (hard=false) Apr-09 13:17:58.615 [main] INFO nextflow.Nextflow - -[nf-core/differentialabundance] Pipeline completed with errors- Apr-09 13:17:58.619 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=6; failedCount=1; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=27.1s; failedDuration=5ms; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=1; peakCpus=1; peakMemory=6 GB; ] Apr-09 13:17:58.619 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file Apr-09 13:17:58.620 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report Apr-09 13:17:59.237 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline Apr-09 13:17:59.496 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done Apr-09 13:17:59.496 [main] INFO org.pf4j.AbstractPluginManager - Stop plugin '[email protected]' Apr-09 13:17:59.496 [main] DEBUG nextflow.plugin.BasePlugin - Plugin stopped nf-validation Apr-09 13:17:59.508 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'FileTransfer' shutdown completed (hard=false) Apr-09 13:17:59.509 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye

System information

Nextflow: 23.10.1 Hardware: Workstation Executor: Slurm Container Image: singularity OS: RHEL 9.3 Version of nf-core/differentialabundance : 1.4.0

acpicornell avatar Apr 09 '24 11:04 acpicornell

Hello, I think I've encountered the same GSEA issue, please see below. The workflow runs fine when GSEA is not invoked. Please note that the GTF is dog, but the GMT is human - I don't think this should cause issues though, as gene symbol is largely in common between the two species.

Thanks, and all the best. Aaron.

nextflow run nf-core/differentialabundance -r 1.4.0\
-profile rnaseq,singularity\
--input c2bbe1-samplesheet.csv\
--contrasts c2bbe1-contrasts.csv\
--matrix nf-core_rnaseq_canfam6/star_salmon/salmon.merged.gene_counts_length_scaled.tsv\
--gtf /projects/health_sciences/ric/ogf/ngs/refs/dog/canfam6/GCF_000002285.5_Dog10K_Boxer_Tasha_genomic.gtf\
--outdir nf-core_diffabun_gsea_hall\
--gsea_run\
--gsea_gene_sets h.all.v2023.2.Hs.symbols.gmt\

N E X T F L O W ~ version 23.10.1 Launching https://github.com/nf-core/differentialabundance [pedantic_mirzakhani] DSL2 - revision: a3d664c12c [1.4.0]

                                    ,--./,-.
    ___     __   __   __   ___     /,-._.--~'

|\ | |__ __ / / \ |__) |__ } { | \| | \__, \__/ | \ |___ \-.,--, .,._,' nf-core/differentialabundance v1.4.0-ga3d664c

Core Nextflow options revision : 1.4.0 runName : pedantic_mirzakhani containerEngine : singularity container : [RMARKDOWNNOTEBOOK:biocontainers/r-shinyngs:1.8.4--r43hdfd78af_0] launchDir : /projects/health_sciences/ric/ogf/ngs/illumina/rna-seq/c2bbe1 workDir : /projects/health_sciences/ric/ogf/ngs/illumina/rna-seq/c2bbe1/work projectDir : /home/jefaa92p/.nextflow/assets/nf-core/differentialabundance userName : jefaa92p profile : rnaseq,singularity configFiles :

Input/output options input : c2bbe1-samplesheet.csv contrasts : c2bbe1-contrasts.csv outdir : nf-core_diffabun_gsea_hall

Abundance values matrix : nf-core_rnaseq_canfam6/star_salmon/salmon.merged.gene_counts_length_scaled.tsv affy_cel_files_archive : null querygse : null

Affy input options affy_cdfname : null

Proteus input options proteus_round_digits : -1

Filtering filtering_min_abundance : 1 filtering_min_samples : 1

Differential analysis differential_min_fold_change: 2 differential_max_pval : 1

Limma specific options (microarray only) limma_spacing : null limma_block : null limma_correlation : null limma_p_value : 1

GSEA gsea_run : true gsea_gene_sets : h.all.v2023.2.Hs.symbols.gmt

Shiny app settings shinyngs_shinyapps_account : null shinyngs_shinyapps_app_name : null

Reporting options report_file : /home/jefaa92p/.nextflow/assets/nf-core/differentialabundance/assets/differentialabundance_report.Rmd logo_file : /home/jefaa92p/.nextflow/assets/nf-core/differentialabundance/docs/images/nf-core-differentialabundance_logo_light.png css_file : /home/jefaa92p/.nextflow/assets/nf-core/differentialabundance/assets/nf-core_style.css citations_file : /home/jefaa92p/.nextflow/assets/nf-core/differentialabundance/CITATIONS.md report_title : null report_author : null report_description : null

Reference genome options gtf : /projects/health_sciences/ric/ogf/ngs/refs/dog/canfam6/GCF_000002285.5_Dog10K_Boxer_Tasha_genomic.gtf

Institutional config options config_profile_name : RNA-seq profile config_profile_description : Settings for RNA-seq analysis

!! Only displaying parameters that differ from the pipeline defaults !!

If you use nf-core/differentialabundance for your analysis please cite:

  • The pipeline https://doi.org/10.5281/zenodo.7568000

  • The nf-core framework https://doi.org/10.1038/s41587-020-0439-x

  • Software dependencies https://github.com/nf-core/differentialabundance/blob/master/CITATIONS.md

executor > slurm (5) [3b/8a7e65] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:GTF_TO_TABLE (GCF_000002285) [100%] 1 of 1 ✔ [50/f6a435] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:VALIDATOR (c2bbe1-samplesheet.csv) [100%] 1 of 1 ✔ [5c/8521c4] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_MATRIXFILTER ([id:study]) [ 0%] 0 of 1 [- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:DESEQ2_NORM - [- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:DESEQ2_DIFFERENTIAL - [- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_TABULARTOGSEAGCT - [01/6d36ef] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_TABULARTOGSEACLS (condition_control_treated) [ 0%] 0 of 1 [d7/3314d6] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:TABULAR_TO_GSEA_CHIP (1) [ 0%] 0 of 1 [- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:GSEA_GSEA - [- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_EXPLORATORY - [- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_DIFFERENTIAL - [- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_DUMPSOFTWAREVERSIONS - [- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:SHINYNGS_APP - [- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:RMARKDOWNNOTEBOOK - [- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:MAKE_REPORT_BUNDLE - ERROR ~ Error executing process > 'NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:TABULAR_TO_GSEA_CHIP (1)'

Caused by: executor > slurm (5) [3b/8a7e65] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:GTF_TO_TABLE (GCF_000002285) [100%] 1 of 1 ✔ [50/f6a435] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:VALIDATOR (c2bbe1-samplesheet.csv) [100%] 1 of 1 ✔ [5c/8521c4] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_MATRIXFILTER ([id:study]) [100%] 1 of 1 ✔ [- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:DESEQ2_NORM - [- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:DESEQ2_DIFFERENTIAL - [- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_TABULARTOGSEAGCT - [01/6d36ef] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_TABULARTOGSEACLS (condition_control_treated) [100%] 1 of 1 ✔ [d7/3314d6] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:TABULAR_TO_GSEA_CHIP (1) [100%] 1 of 1, failed: 1 ✘ [- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:GSEA_GSEA - [- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_EXPLORATORY - [- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_DIFFERENTIAL - [- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_DUMPSOFTWAREVERSIONS - [- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:SHINYNGS_APP - [- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:RMARKDOWNNOTEBOOK - [- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:MAKE_REPORT_BUNDLE - Execution cancelled -- Finishing pending tasks before exit ERROR ~ Error executing process > 'NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:TABULAR_TO_GSEA_CHIP (1)'

Caused by: Process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:TABULAR_TO_GSEA_CHIP (1) terminated with an error exit status (1)

executor > slurm (5) [3b/8a7e65] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:GTF_TO_TABLE (GCF_000002285) [100%] 1 of 1 ✔ [50/f6a435] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:VALIDATOR (c2bbe1-samplesheet.csv) [100%] 1 of 1 ✔ [5c/8521c4] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_MATRIXFILTER ([id:study]) [100%] 1 of 1 ✔ [- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:DESEQ2_NORM - [- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:DESEQ2_DIFFERENTIAL - [- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_TABULARTOGSEAGCT - [01/6d36ef] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_TABULARTOGSEACLS (condition_control_treated) [100%] 1 of 1 ✔ [d7/3314d6] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:TABULAR_TO_GSEA_CHIP (1) [100%] 1 of 1, failed: 1 ✘ [- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:GSEA_GSEA - [- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_EXPLORATORY - [- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_DIFFERENTIAL - [- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_DUMPSOFTWAREVERSIONS - [- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:SHINYNGS_APP - [- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:RMARKDOWNNOTEBOOK - [- ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:MAKE_REPORT_BUNDLE -

ERROR ~ Error executing process > 'NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:TABULAR_TO_GSEA_CHIP (1)'

Caused by: Process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:TABULAR_TO_GSEA_CHIP (1) terminated with an error exit status (1)

Command executed:

function find_column_number { file=$1 column=$2

  head -n 1 $file | tr '\t' '\n' | grep -n "^${column}$" | awk -F':' '{print $1}'

}

id_col=$(find_column_number GCF_000002285.anno.feature_metadata.tsv gene_id) symbol_col=$(find_column_number GCF_000002285.anno.feature_metadata.tsv gene_name) outfile=$(echo GCF_000002285.anno.feature_metadata.tsv | sed 's/(.)../\1/').chip

echo -e "Probe Set ID\tGene Symbol\tGene Title" > ${outfile}.tmp tail -n +2 GCF_000002285.anno.feature_metadata.tsv | awk -F'\t' -v id=$id_col -v symbol=$symbol_col '{print $id"\t"$symbol"\tNA"}' >> ${outfile}.tmp mv ${outfile}.tmp ${outfile}

cat <<-END_VERSIONS > versions.yml "NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:TABULAR_TO_GSEA_CHIP": bash: $(echo $(bash --version | grep -Eo 'version [[:alnum:].]+' | sed 's/version //')) END_VERSIONS

Command exit status: 1

Command output: (empty)

Command error: INFO: Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred INFO: Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred INFO: Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred WARNING: Skipping mount /var/apptainer/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container

Work dir: /projects/health_sciences/ric/ogf/ngs/illumina/rna-seq/c2bbe1/work/d7/3314d6616f60deb8356fcb2ca7ea6d

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named .command.sh

-- Check '.nextflow.log' file for details

ajeffs avatar May 08 '24 03:05 ajeffs

hello! I also run into this problem and got solved by setting --features_name_col gene_id since my input data only has gene_id column but not gene_name. (see https://nfcore.slack.com/archives/C045UNCS5R9/p1721918979101339).

This is a very annoying problem though, and probably many people don't realize when running...

suzannejin avatar Oct 10 '24 13:10 suzannejin