Nextflow workflow report

[insane_wozniak]

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=$(find_column_number GCF_002022765.anno.feature_metadata.tsv gene_id)
  symbol_col=$(find_column_number GCF_002022765.anno.feature_metadata.tsv gene_name)
  outfile=$(echo GCF_002022765.anno.feature_metadata.tsv | sed 's/\(.*\)\..*/\1/').chip
  
  echo -e "Probe Set ID\tGene Symbol\tGene Title" > ${outfile}.tmp
  tail -n +2 GCF_002022765.anno.feature_metadata.tsv | awk -F'\t' -v id=$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

Work dir:
  /mmfs1/gscratch/scrubbed/strigg/analyses/20250804_diffabund/work/ae/962e74cd208135236534481398972d

Container:
  /gscratch/scrubbed/srlab/.apptainer/depot.galaxyproject.org-singularity-gawk-5.1.0.img

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`

Run times

05-Aug-2025 07:34:40 - 05-Aug-2025 08:38:29 (duration: 1h 3m 49s)

  11 succeeded  

  0 cached  

  0 ignored  

  1 failed (3 retries)  

Nextflow command

nextflow run nf-core/differentialabundance -c /gscratch/srlab/strigg/bin/uw_hyak_srlab.config -resume --study_name dataset_2 --input study2_samplesheet.csv --contrasts study2_contrasts.csv --outdir /gscratch/scrubbed/strigg/analyses/20250804_diffabund --matrix salmon.merged.gene_counts_length_scaled_dataset2.tsv --feature_type gene --features_gtf_feature_type gene --filtering_min_abundance 10 --filtering_min_proportion 0.75 --gtf /gscratch/srlab/strigg/GENOMES/GCF_002022765.2_C_virginica-3.0_genomic_noEmptyGeneIDs.gtf --gsea_run true --gene_sets_files /gscratch/srlab/strigg/GENOMES/4706222.C_virginica_named_filtered_depth3_enrichednames.gmt

CPU-Hours

0.1 (11.7% failed)

Launch directory

/mmfs1/gscratch/scrubbed/strigg/analyses/20250804_diffabund

Work directory

/mmfs1/gscratch/scrubbed/strigg/analyses/20250804_diffabund/work

Project directory

/mmfs1/home/strigg/.nextflow/assets/nf-core/differentialabundance

Script name

main.nf

Script ID

245bb78a7f289adc8d5fe330165781c1

Workflow session

b06ad2c0-6caa-4c7f-858a-79ff1af69184

Workflow repository

https://github.com/nf-core/differentialabundance, revision master (commit hash 3dd360fed0dca1780db1bdf5dce85e5258fa2253)

Workflow profile

standard

Workflow container

[RMARKDOWNNOTEBOOK:biocontainers/r-shinyngs:1.8.8--r43hdfd78af_0]

Container engine

singularity

Nextflow version

version 25.04.6, build 5954 (01-07-2025 11:27 UTC)