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Error in TABULAR_TO_GSEA_CHIP #258

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acpicornell opened this issue Apr 9, 2024 · 2 comments
Open

Error in TABULAR_TO_GSEA_CHIP #258

acpicornell opened this issue Apr 9, 2024 · 2 comments
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bug Something isn't working

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@acpicornell
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acpicornell commented Apr 9, 2024 •
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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:

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 acpicornell added the bug Something isn't working label Apr 9, 2024
@ajeffs
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ajeffs commented May 8, 2024

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: a3d664c [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:

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

@suzannejin
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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...

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@ajeffs @acpicornell @suzannejin