ERROR ~ Error executing process > 'NFCORE_RNASPLICE:RNASPLICE:DRIMSEQ_DEXSEQ_DTU_SALMON:DRIMSEQ_FILTER (1)'

[IanCodes]

Description of the bug

My aim was to run rnasplice to output results for SUPPA2. It is not clear whether the following is an error on my part, or there are no significant results. !No genes left after filtering! makes we think it is the latter, but your opinion would be welcome. I am happy to provide more information if it help.

Command used and terminal output

Command line:
nextflow run nf-core/rnasplice --input samplesheet_fastqs_minus.csv --contrasts contrastsheet_minus.csv --outdir RNA-seq_fastqs_minus_samples -profile singularity -r 1.0.2 --rmats --source fastq --fasta Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fa --gtf Saccharomyces_cerevisiae.R64-1-1.111.gtf --miso_genes <redacted> --aligner star_salmon --rmats_read_len 139

Output:
ERROR ~ Error executing process > 'NFCORE_RNASPLICE:RNASPLICE:DRIMSEQ_DEXSEQ_DTU_SALMON:DRIMSEQ_FILTER (1)'

Caused by:
  Process `NFCORE_RNASPLICE:RNASPLICE:DRIMSEQ_DEXSEQ_DTU_SALMON:DRIMSEQ_FILTER (1)` terminated with an error exit status (1)

Command executed:

  run_drimseq_filter.R salmon.merged.txi.dtu.rds tximport.tx2gene.tsv samplesheet_fastqs_minus.csv \
      4 \
      2 \
      2 \
      10 \
      0.1 \
      10
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_RNASPLICE:RNASPLICE:DRIMSEQ_DEXSEQ_DTU_SALMON:DRIMSEQ_FILTER":
      r-base: $(echo $(R --version 2>&1) | sed 's/^.*R version //; s/ .*$//')
      bioconductor-drimseq: $(Rscript -e "library(DRIMSeq); cat(as.character(packageVersion('DRIMSeq')))")
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  INFO:    Converting SIF file to temporary sandbox...
  WARNING: Skipping mount /usr/local/singularity-ce-3.11.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container
  
  Attaching package: 'DRIMSeq'
  
  The following object is masked from 'package:base':
  
      proportions
  
  Error in dmDS_filter(counts = x@counts, min_samps_gene_expr = min_samps_gene_expr,  : 
    !No genes left after filtering!
  Calls: <Anonymous> -> <Anonymous> -> .local -> dmDS_filter
  Execution halted
  INFO:    Cleaning up image...

Work dir:
  <redacted>/work/69/970b0a2cad7dab41066bb18623d068

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

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

Relevant files

No response

System information

nextflow version 23.04.1.5866, run locally on server singularity container 3.11.2 Linux Ubuntu 22.04.3 LTS nf-core/rnasplice 1.0.2