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jma1991 avatar jma1991 commented on August 19, 2024 1

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

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bensouthgate avatar bensouthgate commented on August 19, 2024 1

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.

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jma1991 avatar jma1991 commented on August 19, 2024

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.

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paolo-kunderfranco avatar paolo-kunderfranco commented on August 19, 2024

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

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jma1991 avatar jma1991 commented on August 19, 2024

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.

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paolo-kunderfranco avatar paolo-kunderfranco commented on August 19, 2024

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 ?

`

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paolo-kunderfranco avatar paolo-kunderfranco commented on August 19, 2024

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

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paolo-kunderfranco avatar paolo-kunderfranco commented on August 19, 2024

any suggestion??

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bensouthgate avatar bensouthgate commented on August 19, 2024

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.

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paolo-kunderfranco avatar paolo-kunderfranco commented on August 19, 2024

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

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