Issue with DESEQ2_QC_SALMON step

[pditommaso]

Description of the bug

I've experienced an unexpected problem with DESEQ2_QC_SALMON step. The problem seems caused but a failure in the corresponding deseq2_qc.r R script.

The process stops with the following error message

Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    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, which.max, which.min


Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
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")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians


Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply, rowsum

Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 'ncol': non-numeric variable(s) in data frame: gene_name
Calls: DESeqDataSetFromMatrix -> stopifnot -> ncol -> Math.data.frame
Execution halted

The relevant message looks the following:

Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 'ncol': non-numeric variable(s) in data frame: gene_name

which point to this R script line

https://github.com/nf-core/rnaseq/blob/master/bin/deseq2_qc.r#L58

At this links there's a similar error report, tho not sure how much is related

Command used and terminal output

nextflow run 'https://github.com/nf-core/rnaseq'
		 -name backstabbing_mercator
		 -params-file 'https://scratch.staging-tower.xyz/api/ephemeral/p7jk9gjjGsxM43aSL_14Sg.yaml'
		 -with-tower 'https://scratch.staging-tower.xyz/api'
		 -r 646723c70f04ee6d66391758b02822d4f0fe2966
		 -profile test
		 -resume c09b005d-719b-43a8-a6de-6d326897674b

Relevant files

nextflow.config.txt
params.txt

No response

System information

No response

[pditommaso]

These are the input files of the failing task:

salmon-task.zip

You can even run in your own computer with this command

 docker run --rm \
   --platform linux/amd64 \
   -e AWS_REGION=eu-west-1 \
   -e AWS_ACCESS_KEY_ID=$AWS_ACCESS_KEY_ID \
   -e AWS_SECRET_ACCESS_KEY=$AWS_SECRET_ACCESS_KEY \
   -e NXF_FUSION_BUCKETS=s3://nextflow-ci \
   --privileged  \
   -it \
   reg.staging-tower.xyz/tw/of2wc6jonfxs6ytjn5rw63tumfuw4zlsom/mulled-v2-8849acf39a43cdd6c839a369a74c0adc823e2f91:ab110436faf952a33575c64dd74615a84011450b-0 \
   /bin/bash /fusion/s3/nextflow-ci/scratch/4UEEvCksfgCR8x/d0/e51b513fe3d71382012593750336fc/

[drpatelh]

Looks like a duplicate of #754 which should have been fixed in v3.6.

[drpatelh]

Will close this because I don't think we have seen this issue again with version 3.6. Feel free to re-open if it resurfaces.