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Attempt solving #155

Open nictru opened this issue 1 year ago • 7 comments

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

nictru avatar Jul 12 '24 08:07 nictru

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

nictru avatar Jul 12 '24 08:07 nictru

nf-core lint overall result: Passed :white_check_mark: :warning:

Posted for pipeline commit b33d774

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

:heavy_exclamation_mark: Test warnings:

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

:white_check_mark: Tests passed:

Run details

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

github-actions[bot] avatar Jul 12 '24 08:07 github-actions[bot]

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).

ZabalaAitor avatar Jul 12 '24 11:07 ZabalaAitor

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

nictru avatar Jul 12 '24 14:07 nictru

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

nictru avatar Jul 15 '24 17:07 nictru

Here is the slurm.docx with a new error.

ZabalaAitor avatar Jul 20 '24 12:07 ZabalaAitor

@ nictru , @ZabalaAitor, how is this going? should be update this or is not relevant any more? Thanks!

PS:we are doing spring cleaning , sorry for the pings

lpantano avatar Mar 11 '25 15:03 lpantano

I think this is outdated

nictru avatar Apr 22 '25 17:04 nictru