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nf-core / atacseq

ATAC-seq peak-calling and QC analysis pipeline
https://nf-co.re/atacseq
MIT License
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Errors in MERGED_LIBRARY_BAM_TO_BIGWIG:UCSC_BEDGRAPHTOBIGWIG #290

Closed AAAAAbetter closed 1 year ago

AAAAAbetter commented 1 year ago

Description of the bug

When I run to this step of BAM_TO_BIGWIG, it says the following error, how can I solve this?

Command used and terminal output

Error executing process > 'NFCORE_ATACSEQ:ATACSEQ:MERGED_LIBRARY_BAM_TO_BIGWIG:UCSC_BEDGRAPHTOBIGWIG (control_REP1)'

Caused by:
  Process `NFCORE_ATACSEQ:ATACSEQ:MERGED_LIBRARY_BAM_TO_BIGWIG:UCSC_BEDGRAPHTOBIGWIG (control_REP1)` terminated with an error exit status (255)

Command executed:

  bedGraphToBigWig \
      control_REP1.mLb.clN.bedGraph \
      GRCh38.primary_assembly.genome.fa.sizes \
      control_REP1.mLb.clN.bigWig

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_ATACSEQ:ATACSEQ:MERGED_LIBRARY_BAM_TO_BIGWIG:UCSC_BEDGRAPHTOBIGWIG":
      ucsc: 377
  END_VERSIONS

Command exit status:
  255

Command output:
  (empty)

Command error:
  control_REP1.mLb.clN.bedGraph is not case-sensitive sorted at line 12791860.  Please use "sort -k1,1 -k2,2n" with LC_COLLATE=C,  or bedSort and try again.

Work dir:
  /home/data/yaoyanxin/ABC_model_20230608/nf-ATAC/work/d3/28b5fcda3e5ae068adeba1c121dcb1

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

Relevant files

.nextflow.log

System information

nf-core/atac-seq 2.0

JoseEspinosa commented 1 year ago

This seems to be an error related to your environment variables settings. See here. Also, we had a similar issue on the rnaseq pipeline some time ago, fixed on this PR. You could try to set LANG=C or LC_COLLATE=C and see whether it works.

JoseEspinosa commented 1 year ago

This should be fixed now in dev, in case you want to give it a try

AAAAAbetter commented 1 year ago

This should be fixed now in dev, in case you want to give it a try

Yes! Thanks for your help, I have successfully run this pipline!

JoseEspinosa commented 1 year ago

OK, thanks for reporting back, then I will close the issue now, let us know if you have any further question.