Error executing process > 'NFCORE_CIRCDNA:CIRCDNA:CIRCLEMAP_REALIGN

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

Start with the CIRCLEMAP_REALIGN process command and the .nextflow.log file, then inspect the reported work directory. Focus on the missing index for circDNA_cov15.qname.sorted.bam, the filename discrepancy, and the expected *.bed output. Done means the process completes reliably and produces the expected BED file without the reported missing-file error.