Error executing process > 'NFCORE_CIRCDNA:CIRCDNA:CIRCLEMAP_REALIGN

[ZabalaAitor]

Description of the bug

Hello,

I'm reaching out regarding an intermittent error I've been encountering in my workflow. Specifically, I've observed that on occasion, a particular sample runs smoothly, while other times it fails. Additionally, upon rerunning the script, there are instances where it executes successfully.

It appears that the root of the problem may stem from the filename inconsistency. The file in question, "DNA.circular_read_candidates.bam," seems to occasionally be referenced incorrectly as "DNA.circular_read_candidates.circular_read_candidates.bam."

I would greatly appreciate any guidance or assistance you can provide in resolving this issue.

Command used and terminal output

ERROR ~ Error executing process > 'NFCORE_CIRCDNA:CIRCDNA:CIRCLEMAP_REALIGN (circDNA_cov15)'

Caused by:
  Missing output file(s) `*.bed` expected by process `NFCORE_CIRCDNA:CIRCDNA:CIRCLEMAP_REALIGN (circDNA_cov15)`

Command executed:

  circle_map.py \
      Realign \
       \
      -i circDNA_cov15.circular_read_candidates.sorted.bam \
      -qbam circDNA_cov15.qname.sorted.bam \
      -sbam circDNA_cov15.md.bam \
      -fasta genome.fasta \
      --threads 12 \
      -o circDNA_cov15_circularDNA_coordinates.bed

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_CIRCDNA:CIRCDNA:CIRCLEMAP_REALIGN":
      Circle-Map: $(echo $(circle_map.py --help 2<&1 | grep -o "version=[0-9].[0-9].[0-9]" | sed 's/version=//g'))
  END_VERSIONS

Command exit status:
  0

Command output:
  2024-04-19 11:12:01: Realigning reads using Circle-Map

  2024-04-19 11:12:01: Clustering structural variant reads

  2024-04-19 11:12:09: Splitting clusters to to processors

  2024-04-19 11:12:22: An error happenend during execution. Exiting

Command error:
  [E::idx_find_and_load] Could not retrieve index file for 'circDNA_cov15.qname.sorted.bam'

    0%|          | 0/1200 [00:00<?, ?it/s]

    0%|          | 1/1200 [00:12<4:05:32, 12.29s/it]
    0%|          | 1/1200 [00:12<4:06:14, 12.32s/it]

  0it [00:12, ?it/s]

Work dir:
  /scratch/azabala/work_circdna_short/ed/9b33357cb56bccecc18bb2193ff18a

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

 -- Check '.nextflow.log' file for details

Relevant files

No response

System information

No response

[DSchreyer]

Hi @ZabalaAitor ,
Thank you for detailing your issue.
sorry for the late response. I don't think this is related to the pipeline, but originates from the circle-map software. I encountered this issue also with some of my samples.

"DNA.circular_read_candidates.circular_read_candidates.bam." - where did you get this info from? can you send me the work directory ls and the .command.sh of such a process that fails?

Best regards,
Daniel

[ZabalaAitor]

Hi @DSchreyer,

Thank you for your response and understanding.

I obtained "DNA.circular_read_candidates.circular_read_candidates.bam" from the work directory. Unfortunately, I no longer have access to the work folder, so I cannot provide you with the .command.sh. However, if you encounter the same error, the conflicting file should be in the work directory mentioned in the error code (for example: /scratch/azabala/work_circdna_short/ed/9b33357cb56bccecc18bb2193ff18a).

I will re-run some samples with circle-map to gather the information you requested. It's strange that the script sometimes works well, and the error can be resolved by running it multiple times. Additionally, I have only encountered this issue when using circle-map in nf-core/circdna; it worked fine when run outside nf-core/circdna.

Thank you again for your time and assistance.

Best regards,
Aitor Zabala