Run methylseq with singularity fails! about methylseq

[efratushava]

Trying to pull the singularity image myself, and run
nextflow -log methylseq_try run nf-core/methylseq  -with-singularity /tmp/ekushele-singularity/nfcore-methylseq.img -profile test

Gives out the following error for few times:

Error executing process > 'get_software_versions'

Caused by:
  Process `get_software_versions` terminated with an error exit status (255)

Command executed:

  echo "1.4" &> v_ngi_methylseq.txt
  echo "19.10.0" &> v_nextflow.txt
  bismark_genome_preparation --version &> v_bismark_genome_preparation.txt

And at the end:

Error executing process > 'get_software_versions'

Caused by:
  Process `get_software_versions` terminated with an error exit status (255)

Command executed:

  echo "1.4" &> v_ngi_methylseq.txt
  echo "19.10.0" &> v_nextflow.txt
  bismark_genome_preparation --version &> v_bismark_genome_preparation.txt
  fastqc --version &> v_fastqc.txt
  cutadapt --version &> v_cutadapt.txt
  trim_galore --version &> v_trim_galore.txt
  bismark --version &> v_bismark.txt
  deduplicate_bismark --version &> v_deduplicate_bismark.txt
  bismark_methylation_extractor --version &> v_bismark_methylation_extractor.txt
  bismark2report --version &> v_bismark2report.txt
  bismark2summary --version &> v_bismark2summary.txt
  samtools --version &> v_samtools.txt
  hisat2 --version &> v_hisat2.txt
  bwa &> v_bwa.txt 2>&1 || true
  bwameth.py --version &> v_bwameth.txt
  picard MarkDuplicates --version &> v_picard_markdups.txt 2>&1 || true
  MethylDackel --version &> v_methyldackel.txt
  qualimap --version &> v_qualimap.txt || true
  preseq &> v_preseq.txt
  multiqc --version &> v_multiqc.txt
  scrape_software_versions.py &> software_versions_mqc.yaml

Command exit status:
  255

Command output:
  (empty)

Work dir:
  /my/home/path/work/14/65b67369db4b9fe881d4077eaa3394

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

Trying to look inside my work-dir I found out that there are only the first 8 files (v_ngi_methylseq.txt,v_nextflow.txt,v_bismark_genome_preparation.txt,v_fastqc.txt,v_cutadapt.txt,v_trim_galore.txt,v_bismark.txt,v_deduplicate_bismark.txt), and that the last file contains the following:

>cat /my/home/path/work/14/65b67369db4b9fe881d4077eaa3394/v_deduplicate_bismark.txt
Unknown option: version
Please respecify command line options

I think that what causes the problem.
Can you please help me?

[ewels]

Hi @efratushava,

This sounds very strange. The error log suggests a problem with the bismark_methylation_extractor version command, but any problems in the pipeline regarding that should show up immediately in the CI tests.

Could you please try running the commands manually inside the singularity container?

singularity shell /tmp/ekushele-singularity/nfcore-methylseq.img
bismark_methylation_extractor --version

Phil

[ewels]

Closing due to lack of response.