Error in DRIMSeq::dmDSdata(counts = counts, samples = samps)

[GimenaA]

Description of the bug

I'm getting an error with DRIMSeq when I try to run rnasplice. The pipeline works fine with other samples, so I'm not sure what's causing this error.

Command used and terminal output

Command Used:
nextflow run nf-core/rnasplice -profile docker -params-file /path/to/params.yaml

Error message:
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 Arc_RIPseq-samplesheet.csv \
      6 \
      3 \
      3 \
      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:

  Attaching package: 'DRIMSeq'

  The following object is masked from 'package:base':

      proportions

  Error in DRIMSeq::dmDSdata(counts = counts, samples = samps) : 
    all(samples$sample_id %in% colnames(counts)) is not TRUE
  Calls: <Anonymous> -> stopifnot
  Execution halted

Relevant files

Samplesheet file: sample,fastq_1,fastq_2,strandedness,condition ID11-IP-Arc-R2,/path/to/rawdata/ID11-IP-Arc-R2_1.fastq.gz,/path/to/rawdata/ID11-IP-Arc-R2_2.fastq.gz,unstranded,treatment IP-Arc-R1,/path/to/rawdata/IP-Arc-R1_1.fastq.gz,/path/to/rawdata/IP-Arc-R1_2.fastq.gz,unstranded,treatment ID-2-Arc-IP-R3,/path/to/rawdata/ID-2-Arc-IP-R3_1.fastq.gz,/path/to/rawdata/ID-2-Arc-IP-R3_2.fastq.gz,unstranded,treatment ID-5-Non-IP-R3,/path/to/rawdata/ID-5-Non-IP-R3_1.fastq.gz,/path/to/rawdata/ID-5-Non-IP-R3_2.fastq.gz,unstranded,Control ID12-Non-Arc-R2,/path/to/rawdata/ID12-Non-Arc-R2_1.fastq.gz,/path/to/rawdata/ID12-Non-Arc-R2_2.fastq.gz,unstranded,Control Non-Arc-R1,/path/to/rawdata/Non-Arc-R1_1.fastq.gz,/path/to/rawdata/Non-Arc-R1_2.fastq.gz,unstranded,Control

params.yaml file: input: '/path/to/sequencing_data/Arc_RIPseq-samplesheet.csv' contrasts: '/path/to/sequencing_data/Arc_RIPseq-contrastsheet.csv' outdir: '/path/to/sequencing_data/' fasta: '/home/gimena/reference_files/BDGP6.32_ensemble/Drosophila_melanogaster.BDGP6.32.dna.toplevel.fa' gtf: '/home/gimena/reference_files/GTF_files/fromEnsembl/Drosophila_melanogaster.BDGP6.32.106.gtf' source: 'fastq' aligner: 'star_salmon' min_samps_gene_expr: 6 min_gene_expr: 10 min_samps_feature_expr: 3 min_feature_expr: 10 min_samps_feature_prop: 3 min_feature_prop: 0.1 sashimi_plot: true fig_height: 20 fig_width: 20 miso_genes: FBgn0265487 skip_bigwig: false dexseq_dtu: true suppa: false edger_exon: false dexseq_exon: false rmats: false

System information

Nextflow Version: version 23.10.0 Linux OS Version of nf-core/rnasplice 1.0.1

[pothepanda09]

I'm also running into the same issue! I thought it was the minimum sample/feature tags, so I set it to zero: min_samps_gene_expr: 0 min_gene_expr: 0 min_samps_feature_expr: 0 min_feature_expr: 0 min_samps_feature_prop: 0 min_feature_prop: 0 That wasn't the issue either, so I'm hoping someone knows how to solve this.

[jma1991]

Hey @GimenaA

Thanks for reporting your issue. Can you please try with the latest release? I have a feeling you are using an older version where we didn't handle sample names with dashes in them correctly. See this PR for details.

[jma1991]

Closing as completed. Please re-open if you are still facing the same issue.