error running nf-core rnaseq test pipeline

[natpinzon]

Check Documentation

I have checked the following places for your error:

• [ X] nf-core website: troubleshooting
• [ X] nf-core/rnaseq pipeline documentation

Description of the bug

Dear members of nf-core nextflow team,
I am trying to launch the test pipeline nf-core rnaseq on the IFB (Institut Francais de Bioinformatique) cluster without success.
Maybe you could help me? I don't have an idea of whats is wrong since other users using the same commands don't get this behaviour. I have an error of invalid class "DESeqDataSet"

Steps to reproduce

Steps to reproduce the behaviour:

1. Command line:
   export projectDir=/shared/home/npinzonrestrepo/.nextflow/assets/nf-core/rnaseq/
export JAVA_LD_LIBRARY_PATH=/shared/ifbstor1/software/miniconda/envs/nextflow-21.04.0/lib/server
export JAVA_HOME=/shared/ifbstor1/software/miniconda/envs/nextflow-21.04.0
module load nextflow/21.04.0
nextflow run nf-core/rnaseq -r 3.2 -profile test,ifb_core -resume

2. See error:

-[nf-core/rnaseq] Pipeline completed with errors-
WARN: To render the execution DAG in the required format it is required to install Graphviz -- See http://www.graphviz.org for more info.
Error executing process > 'NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_SALMON'

Caused by:
  Process `NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_SALMON` terminated with an error exit status (1)

Command executed:

  deseq2_qc.r \
      --count_file salmon.merged.gene_counts_length_scaled.tsv \
      --outdir ./ \
      --cores 2 \
      --id_col 1 --sample_suffix '' --outprefix deseq2 --count_col 3

  if [ -f "R_sessionInfo.log" ]; then
      sed "s/deseq2_pca/salmon_deseq2_pca/g" <deseq2_pca_header.txt >tmp.txt
      sed -i -e "s/DESeq2 PCA/SALMON DESeq2 PCA/g" tmp.txt
      cat tmp.txt *.pca.vals.txt > salmon.pca.vals_mqc.tsv

      sed "s/deseq2_clustering/salmon_deseq2_clustering/g" <deseq2_clustering_header.txt >tmp.txt
      sed -i -e "s/DESeq2 sample/SALMON DESeq2 sample/g" tmp.txt
      cat tmp.txt *.sample.dists.txt > salmon.sample.dists_mqc.tsv
  fi

  Rscript -e "library(DESeq2); write(x=as.character(packageVersion('DESeq2')), file='deseq2.version.txt')"

Command exit status:
  1

Command output:
  (empty)

Command error:
      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

  converting counts to integer mode
  Error in validObject(.Object) :
    invalid class "DESeqDataSet" object: superclass "RectangularData" not defined in the environment of the object's class
  Calls: DESeqDataSetFromMatrix ... DESeqDataSet -> new -> initialize -> initialize -> validObject
  Execution halted

Work dir:
  /shared/ifbstor1/projects/dubii2021/npinzonrestrepo/work/91/e2d5d7218d2a80bd495de767e62736

Expected behaviour

<-- I expected the test pipeline to run and be completed with the IFB core Configuration profile-->

Log files

Have you provided the following extra information/files:

• [X ] The .command.log file from the respective work directory (work/91/e2d5d7218d2a80bd495de767e62736)
  .command.log

• [X ] The .command.err file from the respective work directory (work/91/e2d5d7218d2a80bd495de767e62736)
  command.err.txt

• [X ] The .nextflow.log file
  .nextflow.log

System

• Hardware:
• Executor:
• OS:
• Version

Nextflow Installation

• Version: <-- [nextflow/20.04.1] -->
• Version: <-- [nextflow/21.04.0] -->

Container engine

• Engine: <

-- [ Singularity] -->

• version:
• Image tag:

Additional context

[maxulysse]

@drpatelh any idea what might have caused this issue?

[drpatelh]

I don't I'm afraid. May be worth joining us on Slack in the #rnaseq channel so we can discuss in real-time though? https://nf-co.re/join

[natpinzon]

Hello, thank you very much. I have solved it by changing the name of my ~/R directory. There was the source of conflict.

[maxulysse]

I'm glad the problem was solved.
Don't hesitate if you need anything else