DRIMSEQ_FILTER error

[paolo-kunderfranco]

Description of the bug

Dear All, I am testing the pipeline and I am facing the following error, Not all conditions are included in the contrast file. Thanks for your support

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 q.tx2gene.tsv samplesheet.csv \
      4 \
      2 \
      2 \
      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 .local(x, ...) : 
    min_samps_gene_expr >= 0 && min_samps_gene_expr <= ncol(x@counts) is not TRUE
  Calls: <Anonymous> -> <Anonymous> -> .local -> stopifnot
  Execution halted

Command used and terminal output

nextflow run nf-core/rnasplice --input $wd/samplesheet.csv \
                               --contrasts $wd/contrast.csv \
                               --outdir test \
                               --genome GRCm38 \
                               -profile singularity \
                               --aligner star \
                               --dexseq_exon \
                               --edger_exon \
                               --rmats \
                               --rmats_read_len 75 \
                               --save_reference true \
                               --sashimi_plot true \
                               -config config.config \
                               -r dev

Relevant files

nextflow.log

System information

nextflow/22.10.4 HPC - slurm Operating System: Debian GNU/Linux 10 (buster)

[jma1991]

Hi @paolo-kunderfranco

Please could you try to re-run the pipeline with the following dmFilter parameters set to zero:

• min_samps_gene_expr
• min_samps_feature_expr
• min_samps_feature_prop
• min_feature_expr
• min_feature_prop
• min_gene_expr

This can be done in the nextflow.config file - we are trying to ascertain whether there is a bug or the filters are too stringent for your samples.

[paolo-kunderfranco]

ok now it seems working, but now I am again as always with different pipelines blocked in STAR segmentation error.

[jma1991]

I believe this is a known issue with STAR 2.7.10a but the nf-core modules have not been updated. In the meantime, if you are able to use conda, you can download the pipeline and replace bioconda::star=2.7.10a with bioconda::star=2.7.10b in each of the main.nf files for the STAR modules.

[paolo-kunderfranco]

you mean here? for both genomegenerate and align modules?

`process STAR_ALIGN { tag "$meta.id" label 'process_high'

conda "bioconda::star=2.7.10a bioconda::samtools=1.16.1 conda-forge::gawk=5.1.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

`

[jma1991]

Yes, that's right. Give it a go and report back.

[paolo-kunderfranco]

error still persist

Error executing process > NFCORE_RNASPLICE:RNASPLICE:ALIGN_STAR:STAR_ALIGN_IGENOMES (CP28)
Caused by:
Process NFCORE_RNASPLICE:RNASPLICE:ALIGN_STAR:STAR_ALIGN_IGENOMES (CP28) terminated with an error exit status (139)

Command executed:
  STAR \
      --genomeDir STARIndex \
      --readFilesIn CP28_1_val_1.fq.gz CP28_2_val_2.fq.gz  \
      --runThreadN 16 \
      --outFileNamePrefix CP28. \
       \
      --sjdbGTFfile genes.gtf \
      --outSAMattrRGline ID:CP28 'SM:CP28'   \
      --quantMode TranscriptomeSAM --twopassMode Basic --outSAMtype BAM Unsorted --readFilesCommand gunzip -c --runRNGseed 0 --outFilterMultimapNmax 20 --alignSJDBoverhangMin 1 --outSAMattributes NH HI AS NM MD --quantTranscriptomeBan Singleend

  if [ -f CP28.Unmapped.out.mate1 ]; then
      mv CP28.Unmapped.out.mate1 CP28.unmapped_1.fastq
      gzip CP28.unmapped_1.fastq
  fi
  if [ -f CP28.Unmapped.out.mate2 ]; then
      mv CP28.Unmapped.out.mate2 CP28.unmapped_2.fastq
      gzip CP28.unmapped_2.fastq
  fi
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_RNASPLICE:RNASPLICE:ALIGN_STAR:STAR_ALIGN_IGENOMES":
      star: $(STAR --version | sed -e "s/STAR_//g")
      samtools: $(echo $(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*$//')
      gawk: $(echo $(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/ .*$//')
  END_VERSIONS

Command exit status:
  139

Command output:
  (empty)

Command error:
  .command.sh: line 10: 10242 Segmentation fault      STAR --genomeDir STARIndex --readFilesIn CP28_1_val_1.fq.gz CP28_2_val_2.fq.gz --runThreadN 16 --outFileNamePrefix CP28. --sjdbGTFfile genes.gtf --outSAMattrRGline ID:CP28 'SM:CP28' --quantMode TranscriptomeSAM --twopassMode Basic --outSAMtype BAM Unsorted --readFilesCommand gunzip -c --runRNGseed 0 --outFilterMultimapNmax 20 --alignSJDBoverhangMin 1 --outSAMattributes NH HI AS NM MD --quantTranscriptomeBan Singleend

[paolo-kunderfranco]

any suggestion??

[bensouthgate]

Hi @paolo-kunderfranco are you running with singularity? If so could you try running with conda and the changed versions as @jma1991 suggested? Trying with docker would also give us some useful information.

[paolo-kunderfranco]

Hi @bensouthgate , I succesfully align samples with docker, but failed in SUPPA

[bensouthgate]

Hi @paolo-kunderfranco - if you no longer have an issue with DRIMSEQ_FILTER or STAR_ALIGN are you happy for me to close this issue? I believe we are working on another issue you opened for SUPPA #71.