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_RNASPLICE:RNASPLICE:EDGER_DEU:EDGER_EXON (samplesheet.csv)'

Caused by:
  Process `NFCORE_RNASPLICE:RNASPLICE:EDGER_DEU:EDGER_EXON (samplesheet.csv)` terminated with an error exit status (1)


Command executed:

  run_edger_exon.R featurecounts samplesheet.csv contrastsheet.csv 10
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_RNASPLICE:RNASPLICE:EDGER_DEU:EDGER_EXON":
      r-base: $(echo $(R --version 2>&1) | sed 's/^.*R version //; s/ .*$//')
      bioconductor-edger:  $(Rscript -e "library(edgeR); cat(as.character(packageVersion('edgeR')))")
  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
  Loading required package: limma
  Error in eval(ej, envir = levelsenv) : object 'TREATMENT' not found
  Calls: makeContrasts -> eval -> eval
  Execution halted

Work dir:
  /mmfs1/gscratch/scrubbed/strigg/analyses/20251205_rnasplice_Ptua/work/ef/6d347f430095e18b6e580c07b7a0a6

Container:
  /gscratch/scrubbed/srlab/.apptainer/depot.galaxyproject.org-singularity-mulled-v2-419bd7f10b2b902489ac63bbaafc7db76f8e0ae1-709335c37934db1b481054cbec637c6e5b5971cb-0.img

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line