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Attempt solving #155 #158

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@nictru nictru commented Jul 12, 2024

Tries to solve the problem of CIRIquant not being able to access the GTF file by staging it to the working directory

@nictru nictru linked an issue Jul 12, 2024 that may be closed by this pull request
GTF file not found with CIRIquant #155
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nictru commented Jul 12, 2024

@ZabalaAitor, could you check if this solves your problem?

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github-actions bot commented Jul 12, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit b33d774

+| ✅ 217 tests passed       |+
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-07-15 17:07:04

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ZabalaAitor commented Jul 12, 2024 •
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In this case, it is able to access the GTF file. However, I encountered the following error (which I think should be common for all works, not specific to this one):

ERROR ~ Error executing process > 'NFCORE_CIRCRNA:CIRCRNA:QUANTIFICATION:TRANSCRIPTOME (transcriptome)'

Caused by:
  Process `NFCORE_CIRCRNA:CIRCRNA:QUANTIFICATION:TRANSCRIPTOME (transcriptome)` terminated with an error exit status (1)

Command executed:

  gffread \
      -g genome.fa \
      -w transcriptome.fasta \
       \
      transcriptome.filtered.gtf
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_CIRCRNA:CIRCRNA:QUANTIFICATION:TRANSCRIPTOME":
      gffread: $(gffread --version 2>&1)
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  FASTA index file genome.fa.fai created.
  Warning: couldn't find fasta record for 'chr10_GL383545v1_alt'!
  Error: no genomic sequence available (check -g option!).

I have attached the output file (slurm-506198.txt).

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nictru commented Jul 12, 2024

I am already working on this as someone else has pointed this out before. You can keep track of it via #157

@nictru nictru force-pushed the 155-gtf-file-not-found-with-ciriquant branch from b5931b9 to b33d774 Compare July 15, 2024 17:05
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nictru commented Jul 15, 2024

@ZabalaAitor, the issue you mentioned in your previous message should be fixed now, could you try again?

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Here is the slurm.docx with a new error.

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GTF file not found with CIRIquant
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