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" 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](https://github.com/nf-core/rnaseq/files/6878172/default.command.log)

- [X ] The `.command.err` file from the respective work directory (work/91/e2d5d7218d2a80bd495de767e62736)
[command.err.txt](https://github.com/nf-core/rnaseq/files/6878176/command.err.txt)

- [X ] The `.nextflow.log` file
[.nextflow.log](https://github.com/nf-core/rnaseq/files/6878162/default.nextflow.log)

## System

- Hardware: <!-- [.] -->
- Executor: <!-- [slurm] -->
- OS: <!-- [Linux] -->
- Version <!-- [] -->

## Nextflow Installation

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

## Container engine

- Engine: <

-- [ Singularity] -->
- version: <!-- [e.g. 1.0.0] -->
- Image tag: <!-- [e.g. nfcore/rnaseq:1.0.0] -->

## Additional context

<!-- Add any other context about the problem here. -->

[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