STAGER error: subscript out of bounds

[paolo-kunderfranco]

Description of the bug

Dear All,
As anticipated here, #71, I am now facing an issue with run_stager command. Here are relevant info. Many thks

run_stager.R CP-Brain DEXSeqResults.CP-Brain.tsv perGeneQValue.CP-Brain.tsv dexseq

Command used and terminal output

nextflow run nf-core/rnasplice --input $wd/samplesheet.csv \
							   --contrasts $wd/contrast.csv \
							   --outdir splice_attempt1 \
							   --genome GRCm38 \
							   --aligner star \
							   --min_samps_gene_expr 2 \
							   --min_samps_feature_expr 2 \
							   --min_gene_expr 5 \
							   --min_feature_expr 5 \
							   --min_feature_prop 0.2 \
							   --dexseq_exon true \
							   --edger_exon true\
							   --rmats true \
							   --rmats_read_len 75 \
							   --save_reference true \
							   --sashimi_plot true \
							   -config config.config \
							   -profile docker \
							   -r dev
exit 0




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

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

Command executed:

  run_stager.R CP-Brain DEXSeqResults.CP-Brain.tsv perGeneQValue.CP-Brain.tsv dexseq
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_RNASPLICE:RNASPLICE:DRIMSEQ_DEXSEQ_DTU_SALMON:STAGER":
      r-base: $(echo $(R --version 2>&1) | sed 's/^.*R version //; s/ .*$//')
      bioconductor-stager: $(Rscript -e "library(stageR); cat(as.character(packageVersion('stageR')))")
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
      IQR, mad, sd, var, xtabs
  
  The following objects are masked from 'package:base':
  
      Filter, Find, Map, Position, Reduce, anyDuplicated, append,
      as.data.frame, basename, cbind, colnames, dirname, do.call,
      duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
      lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
      pmin.int, rank, rbind, 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:base':
  
      expand.grid
  
  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: 'stageR'
  
  The following object is masked from 'package:methods':
  
      getMethod
  
  Error in `[<-`(`*tmp*`, idCon, 1, value = unlist(txLevelAdjustments)) : 
    subscript out of bounds
  Calls: stageWiseAdjustment -> stageWiseAdjustment -> .local -> .stageWiseTest
  Execution halted

Relevant files

[nextflow.log](https://github.com/nf-core/rnasplice
splicing_P107513878.log
/files/12173874/nextflow.log)

System information

nextflow/23.04.1
debian 10
slurm
dev version

[jma1991]

Please can you post your sample and contrasts sheet? Additionally, can you try again with the latest dev branch. We have pushed a few fixes in the last couple of days which might be related.

[paolo-kunderfranco]

Here are there, sorry for the delay. Best

contrast.csv
samplesheet.csv

[paolo-kunderfranco]

any suggestion?

[jma1991]

Hi @paolo-kunderfranco - Please could you try with the latest dev branch as suggested in my last reply?

[jma1991]

Closed given no reply. Please re-open if you are still experiencing the error.

[paolo-kunderfranco]

Hi, I just tried the new develop version, and the same error still persist:

N E X T F L O W ~ version 23.04.2
Launching https://github.com/nf-core/rnasplice [big_franklin] DSL2 - revision: 9fe10b0 [dev]