Nextflow workflow report

[elated_bose]

Error executing process > 'NFCORE_RNAVAR:RNAVAR:CAT_FASTQ (ACR-139-TP1)'

Caused by:
  Task 'NFCORE_RNAVAR:RNAVAR:CAT_FASTQ (ACR-139-TP1)' could not be submitted within specified 'maxAwait' time: 1h


Command executed:

  cat input1/ACR-139-TP1_R1_001.fastp-trim.fq.gz > ACR-139-TP1_1.merged.fastq.gz
  cat input2/ACR-139-TP1_R2_001.fastp-trim.fq.gz > ACR-139-TP1_2.merged.fastq.gz
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_RNAVAR:RNAVAR:CAT_FASTQ":
      cat: $(echo $(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*$//')
  END_VERSIONS

Command exit status:
  -

Command output:
  (empty)

Work dir:
  /mmfs1/gscratch/scrubbed/strigg/analyses/20250722_rnavar_Apul/work/5d/cabed3c1b43cfa7013686571ea02f7

Container:
  /gscratch/scrubbed/srlab/.apptainer/community-cr-prod.seqera.io-docker-registry-v2-blobs-sha256-52-52ccce28d2ab928ab862e25aae26314d69c8e38bd41ca9431c67ef05221348aa-data.img

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

Run times

22-Jul-2025 07:18:24 - 22-Jul-2025 10:18:54 (duration: 3h 30s)

  0 succeeded  

  0 cached  

  0 ignored  

  91 failed  

Nextflow command

nextflow run nf-core/rnavar -c /gscratch/srlab/strigg/bin/uw_hyak_srlab.config -resume --input samplesheet.csv --genome null --igenomes_ignore --fasta /gscratch/srlab/strigg/GENOMES/Apulcra-genome.fa --gtf /gscratch/srlab/strigg/GENOMES/Apulchra-genome.gtf --skip_variantannotation --skip_baserecalibration true --outdir result

CPU-Hours

(a few seconds)

Launch directory

/mmfs1/gscratch/scrubbed/strigg/analyses/20250722_rnavar_Apul

Work directory

/mmfs1/gscratch/scrubbed/strigg/analyses/20250722_rnavar_Apul/work

Project directory

/mmfs1/home/strigg/.nextflow/assets/nf-core/rnavar

Script name

main.nf

Script ID

6829325bfeff043a2d4dd1772e7aad18

Workflow session

62adb70e-9ef9-4c37-bc0e-9dd55d7a319d

Workflow repository

https://github.com/nf-core/rnavar, revision master (commit hash 6a5ca7896f12ffc3b8a8c97c21cd0abcd7bf2e36)

Workflow profile

standard

Nextflow version

version 24.10.6, build 5937 (23-04-2025 16:53 UTC)