Nextflow workflow report

Workflow execution completed unsuccessfully!

The exit status of the task that caused the workflow execution to fail was: 1.

The full error message was:

Error executing process > 'NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:VALIDATOR (study1_samplesheet.csv)'

Caused by:
  Process `NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:VALIDATOR (study1_samplesheet.csv)` terminated with an error exit status (1)


Command executed:

  validate_fom_components.R \
      --sample_metadata "study1_samplesheet.csv" \
      --feature_metadata 'GCF_002022765.anno.tsv' \
      --assay_files "salmon.merged.gene_counts_length_scaled_dataset1.tsv" \
      --contrasts_file "study1_contrasts.csv" \
      --output_directory "dataset_1" \
      --sample_id_col 'sample' --feature_id_col 'gene_id'
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:VALIDATOR":
      r-base: $(echo $(R --version 2>&1) | sed 's/^.*R version //; s/ .*$//')
      r-shinyngs: $(Rscript -e "library(shinyngs); cat(as.character(packageVersion('shinyngs')))")
  END_VERSIONS

Command exit status:
  1

Command output:
  [1] "Reading sample sheet at study1_samplesheet.csv with ID col sample"
  [1] "Reading feature metadata at GCF_002022765.anno.tsv with ID col gene_id"
  [1] "Reading assay matrix salmon.merged.gene_counts_length_scaled_dataset1.tsv and validating against samples and features (if supplied)"
  [1] "...  salmon.merged.gene_counts_length_scaled_dataset1.tsv matrix good"
  [1] "Reading contrast definitions and validating against sample sheet"

Command error:
      Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort,
      table, tapply, union, unique, unsplit, which.max, which.min
  
  Loading required package: S4Vectors
  
  Attaching package: ‘S4Vectors’
  
  The following object is masked from ‘package:utils’:
  
      findMatches
  
  The following objects are masked from ‘package:base’:
  
      expand.grid, I, unname
  
  Loading required package: IRanges
  Loading required package: GenomeInfoDb
  Loading required package: Biobase
  Welcome to Bioconductor
  
      Vignettes contain introductory material; view with
      'browseVignettes()'. To cite Bioconductor, see
      'citation("Biobase")', and for packages 'citation("pkgname")'.
  
  
  Attaching package: ‘Biobase’
  
  The following object is masked from ‘package:MatrixGenerics’:
  
      rowMedians
  
  The following objects are masked from ‘package:matrixStats’:
  
      anyMissing, rowMedians
  
  
  Attaching package: ‘shinyngs’
  
  The following object is masked from ‘package:MatrixGenerics’:
  
      colMedians
  
  The following object is masked from ‘package:matrixStats’:
  
      colMedians
  
  Error in checkListIsSubset(val, samples[[var]], "contrast levels", "sample metadata variable") : 
    Not all contrast levels (ABC_VIMS_Family_2017190) are available in the sample metadata variable (ABC_VIMS_Family_2017084,ABC_VIMS_Family_2017089,ABC_VIMS_Family_2017120,ABC_VIMS_Family_2017084,ABC_VIMS_Family_2017084,ABC_VIMS_Family_2017089,ABC_VIMS_Family_2017089,ABC_VIMS_Family_2017090,ABC_VIMS_Family_2017090,ABC_VIMS_Family_2017120,ABC_VIMS_Family_2017089,ABC_VIMS_Family_2017084,ABC_VIMS_Family_2017089,ABC_VIMS_Family_2017090,ABC_VIMS_Family_2017090,ABC_VIMS_Family_2017120,ABC_VIMS_Family_2017084,ABC_VIMS_Family_2017084,ABC_VIMS_Family_2017089,ABC_VIMS_Family_2017090,ABC_VIMS_Family_2017120,ABC_VIMS_Family_2017120,ABC_VIMS_Family_2017084,ABC_VIMS_Family_2017089,ABC_VIMS_Family_2017089,ABC_VIMS_Family_2017090,ABC_VIMS_Family_2017084,ABC_VIMS_Family_2017090,ABC_VIMS_Family_2017120,ABC_VIMS_Family_2017120,ABC_VIMS_Family_2017084,ABC_VIMS_Family_2017084,ABC_VIMS_Family_2017089,ABC_VIMS_Family_2017090,ABC_VIMS_Family_2017090,ABC_VIMS_Family_2017120,ABC_VIMS_Family_2017089,ABC_VI
  Calls: validate_inputs -> read_contrasts -> checkListIsSubset
  Execution halted

Work dir:
  /mmfs1/gscratch/scrubbed/strigg/analyses/20250701_diffabund/work/4f/79875b1c9c90c9d6a02085756a56f8

Container:
  /gscratch/scrubbed/srlab/.apptainer/depot.galaxyproject.org-singularity-r-shinyngs-1.8.8--r43hdfd78af_0.img

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`