[ERRO] open bam_bundles/000000000_chr1:14359:6208325_bundle.bam: invalid argument

[santiago-es]

Operating System

Ubuntu 22.04

Other Linux

No response

Workflow Version

v1.0.0

Workflow Execution

EPI2ME Desktop application

EPI2ME Version

v5.1.8

CLI command run

No response

Workflow Execution - CLI Execution Profile

None

What happened?

running wf-transcriptomes on epi2me desktop and failed during split_bams step due to an "invalid argument" when trying to bundle bams after running for ~3d

Relevant log output

Command executed:
  n=`samtools view -c w_reads_aln_sorted.bam`
  if [[ n -lt 1 ]]
  then
      echo 'There are no reads mapping for w. Exiting!'
      exit 1
  fi

  re='^[0-9]+$'

  if [[ 50000 =~ $re ]]
  then
      echo "Bundling up the bams"
      seqkit bam -j 16 -N 50000 w_reads_aln_sorted.bam -o  bam_bundles/
      let i=1
      for b in bam_bundles/*.bam; do
          echo $b
          newname="w_batch_${i}.bam"
          mv $b $newname
         ((i++))
      done
  else
      echo 'no bundling'
      ln -s w_reads_aln_sorted.bam w_batch_1.bam
  fi
Command exit status:
  255
Command output:
  Bundling up the bams
Command error:
  Bundling up the bams
  [INFO] Creating BAM bundles from file: w_reads_aln_sorted.bam
  [INFO] Minimum reads per bundle: 50000
  [INFO] Output directory: bam_bundles/
  Bundle    Chrom   Start   End NrRecs  NrLoci
  [ERRO] open bam_bundles/000000000_chr1:14359:6208325_bundle.bam: invalid argument
Work dir:
  /media/artandi/Elements/epi2me/instances/wf-transcriptomes_01HKDJFKA0G5DHQCKXD4JYBJRV/work/06/f66f4b0dcf215e95b0f8c93fba9fe4
Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
 -- Check '/media/artandi/Elements/epi2me/instances/wf-transcriptomes_01HKDJFKA0G5DHQCKXD4JYBJRV/nextflow.log' file for details
WARN: Killing running tasks (1)

Application activity log entry

No response

[nrhorner]

Hi @santiago-es

Would you mind posting the full .nextflow.log please

[santiago-es]

nextflow.log

attached above

[santiago-es]

I was able to solve this, and it now runs without issue. I am having some trouble understanding some of the output though.

1. where are the bam files? In another issue I saw these should be output, but I don't see them in any of the out_dir directories or files.
2. what are the merged transcriptome fasta files useful for? Do I need to re-align them to a genome to get a transcriptome bam?
3. is there any way to do differential exon usage and not just transcript usage thanks again for all the help!

[nrhorner]

Hi @santiago-es thanks for letting us know. Please open another ticket with your question regarding output files, if you still have these

[nrhorner]

Hi @santiago-es Could you let me know know how you fixed this issue? We have another user with the same problem.

[santiago-es]

Hey Neil,

In all honesty, I don’t think I remember how I fixed this particular problem haha. I did end up using the cloud based epi2me though instead of Desktop. Perhaps granting the user access to the cloud based epi2me will help?

Best

Santiago On May 24, 2024 at 4:10 AM -0700, Neil Horner @.***>, wrote:

Hi @santiago-es Could you let me know know how you fixed this issue? We have another user with the same problem. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: @.***>

[nrhorner]

Hi Santiago,

It was a while ago, so I knew it was a long shot. Thanks for getting back to with the extra info though.

Cheers,

Neil