Error executing process 'snp:cat_haplotagged_contigs'

[alyazeeditalal]

Operating System

Other Linux (please specify below)

Other Linux

No response

Workflow Version

24.10.1

Workflow Execution

Command line (Cluster)

Other workflow execution

No response

EPI2ME Version

No response

CLI command run

nextflow
run epi2me-labs/wf-human-variation
-c 'scripts/custom.config'
--bam "samples/${sample}/bam/"
--ref 'references/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz'
--bed 'references/human_GRCh38_no_alt_analysis_set.trf.bed'
--out_dir "samples/${sample}/variation_wf" --sample_name "${sample}"
--threads 64
--ubam_map_threads 40
--ubam_sort_threads 16
--ubam_bam2fq_threads 8
--modkit_threads 16
--snp
--sv
--mod
--phased
--override_basecaller_cfg [email protected]
-resume
-profile singularity

Workflow Execution - CLI Execution Profile

None

What happened?

Would you please help me rerun the pipeline?

The pipeline runs perfectly but fails to run through the cat_haplotagged_contigs process even when resumed with large memory (400G) and threads (32).

nextflow.log is attached

nextflow.log

Relevant log output

"Caused by:
  Process `snp:cat_haplotagged_contigs (1)` terminated with an error exit status (1)Command executed:

  # ensure this bit is idempotent as it will inevitably not be called so
  if [ -f seq_list.txt ]; then
      rm seq_list.txt
  fi
  # pick the "first" bam and read its SQ list to determine sort order
  samtools view -H --no-PG `ls *_hp.bam | head -n1` | grep '^@SQ' | sed -nE 's,.*SN:([^[:space:]]*).*,\1,p' > seq_list.txt
  # append present contigs to a file of file names, to cat according to SQ order
  while read sq; do
      if [ -f "${sq}_hp.bam" ]; then
          echo "${sq}_hp.bam" >> cat.fofn
      fi
  done < seq_list.txt
  if [ ! -s cat.fofn ]; then
      echo "No haplotagged inputs to cat? Are the input file names staged correctly?"
      exit 70 # EX_SOFTWARE
  fi
  
  # cat just cats, if we want bam, we'll have to deal with that ourselves
  if [ "cram" = "cram" ]; then
      samtools cat -b cat.fofn --no-PG -o - | samtools view --no-PG -@ 63 --reference ref.fa -O CRAM --write-index -o "GP004.haplotagged.cram##idx##GP004.haplotagged.cram.crai"
  else
      samtools cat -b cat.fofn --no-PG -@ 63 -o "GP004.haplotagged.bam"
      samtools index -@ 63 -b "GP004.haplotagged.bam"
  fi

Command exit status:
  1

Command output:
  (empty)

Command error:
  [W::cram_encode_aux] Missing @RG header for RG "55d1fcf2-75f2-43b3-bd01-d2dcb2fea4be_dna_r10.4.1_e8.2_5khz_400bps_hac@v4.2.0"
  [W::cram_encode_aux] Missing @RG header for RG "55d1fcf2-75f2-43b3-bd01-d2dcb2fea4be_dna_r10.4.1_e8.2_5khz_400bps_hac@v4.2.0"
  [W::cram_encode_aux] Missing @RG header for RG "55d1fcf2-75f2-43b3-bd01-d2dcb2fea4be_dna_r10.4.1_e8.2_5khz_400bps_hac@v4.2.0"
  [W::cram_encode_aux] Missing @RG header for RG "55d1fcf2-75f2-43b3-bd01-d2dcb2fea4be_dna_r10.4.1_e8.2_5khz_400bps_hac@v4.2.0"
  [W::cram_encode_aux] Missing @RG header for RG "55d1fcf2-75f2-43b3-bd01-d2dcb2fea4be_dna_r10.4.1_e8.2_5khz_400bps_hac@v4.2.0"
  [W::cram_encode_aux] Missing @RG header for RG "55d1fcf2-75f2-43b3-bd01-d2dcb2fea4be_dna_r10.4.1_e8.2_5khz_400bps_hac@v4.2.0"
  [W::cram_encode_aux] Missing @RG header for RG "55d1fcf2-75f2-43b3-bd01-d2dcb2fea4be_dna_r10.4.1_e8.2_5khz_400bps_hac@v4.2.0"
  [W::cram_encode_aux] Missing @RG header for RG "55d1fcf2-75f2-43b3-bd01-d2dcb2fea4be_dna_r10.4.1_e8.2_5khz_400bps_hac@v4.2.0"
  [W::cram_encode_aux] Missing @RG header for RG "55d1fcf2-75f2-43b3-bd01-d2dcb2fea4be_dna_r10.4.1_e8.2_5khz_400bps_hac@v4.2.0"
  [W::cram_encode_aux] Missing @RG header for RG "55d1fcf2-75f2-43b3-bd01-d2dcb2fea4be_dna_r10.4.1_e8.2_5khz_400bps_hac@v4.2.0"
  [W::cram_encode_aux] Missing @RG header for RG "55d1fcf2-75f2-43b3-bd01-d2dcb2fea4be_dna_r10.4.1_e8.2_5khz_400bps_hac@v4.2.0"
  [W::cram_encode_aux] Missing @RG header for RG "55d1fcf2-75f2-43b3-bd01-d2dcb2fea4be_dna_r10.4.1_e8.2_5khz_400bps_hac@v4.2.0"
  [W::cram_encode_aux] Missing @RG header for RG "55d1fcf2-75f2-43b3-bd01-d2dcb2fea4be_dna_r10.4.1_e8.2_5khz_400bps_hac@v4.2.0"
  [W::cram_encode_aux] Missing @RG header for RG "55d1fcf2-75f2-43b3-bd01-d2dcb2fea4be_dna_r10.4.1_e8.2_5khz_400bps_hac@v4.2.0"
  [W::cram_encode_aux] Missing @RG header for RG "55d1fcf2-75f2-43b3-bd01-d2dcb2fea4be_dna_r10.4.1_e8.2_5khz_400bps_hac@v4.2.0"
  [W::cram_encode_aux] Missing @RG header for RG "55d1fcf2-75f2-43b3-bd01-d2dcb2fea4be_dna_r10.4.1_e8.2_5khz_400bps_hac@v4.2.0"
  [W::cram_encode_aux] Missing @RG header for RG "55d1fcf2-75f2-43b3-bd01-d2dcb2fea4be_dna_r10.4.1_e8.2_5khz_400bps_hac@v4.2.0"
  [W::cram_encode_aux] Missing @RG header for RG "55d1fcf2-75f2-43b3-bd01-d2dcb2fea4be_dna_r10.4.1_e8.2_5khz_400bps_hac@v4.2.0"
  [W::cram_encode_aux] Missing @RG header for RG "55d1fcf2-75f2-43b3-bd01-d2dcb2fea4be_dna_r10.4.1_e8.2_5khz_400bps_hac@v4.2.0"
  [W::cram_encode_aux] Missing @RG header for RG "55d1fcf2-75f2-43b3-bd01-d2dcb2fea4be_dna_r10.4.1_e8.2_5khz_400bps_hac@v4.2.0"
  [W::cram_encode_aux] Missing @RG header for RG "55d1fcf2-75f2-43b3-bd01-d2dcb2fea4be_dna_r10.4.1_e8.2_5khz_400bps_hac@v4.2.0"
  [W::cram_encode_aux] Missing @RG header for RG "55d1fcf2-75f2-43b3-bd01-d2dcb2fea4be_dna_r10.4.1_e8.2_5khz_400bps_hac@v4.2.0"
  [W::cram_encode_aux] Missing @RG header for RG "55d1fcf2-75f2-43b3-bd01-d2dcb2fea4be_dna_r10.4.1_e8.2_5khz_400bps_hac@v4.2.0"
  [W::cram_encode_aux] Missing @RG header for RG "55d1fcf2-75f2-43b3-bd01-d2dcb2fea4be_dna_r10.4.1_e8.2_5khz_400bps_hac@v4.2.0"
  [W::cram_encode_aux] Missing @RG header for RG "55d1fcf2-75f2-43b3-bd01-d2dcb2fea4be_dna_r10.4.1_e8.2_5khz_400bps_hac@v4.2.0"
  [W::cram_encode_aux] Missing @RG header for RG "55d1fcf2-75f2-43b3-bd01-d2dcb2fea4be_dna_r10.4.1_e8.2_5khz_400bps_hac@v4.2.0"
  [W::cram_encode_aux] Missing @RG header for RG "55d1fcf2-75f2-43b3-bd01-d2dcb2fea4be_dna_r10.4.1_e8.2_5khz_400bps_hac@v4.2.0"
  [W::cram_encode_aux] Missing @RG header for RG "55d1fcf2-75f2-43b3-bd01-d2dcb2fea4be_dna_r10.4.1_e8.2_5khz_400bps_hac@v4.2.0"
  [W::cram_encode_aux] Missing @RG header for RG "55d1fcf2-75f2-43b3-bd01-d2dcb2fea4be_dna_r10.4.1_e8.2_5khz_400bps_hac@v4.2.0"
  [W::cram_encode_aux] Missing @RG header for RG "55d1fcf2-75f2-43b3-bd01-d2dcb2fea4be_dna_r10.4.1_e8.2_5khz_400bps_hac@v4.2.0"
  [W::cram_encode_aux] Missing @RG header for RG "55d1fcf2-75f2-43b3-bd01-d2dcb2fea4be_dna_r10.4.1_e8.2_5khz_400bps_hac@v4.2.0"
  [W::cram_encode_aux] Missing @RG header for RG "55d1fcf2-75f2-43b3-bd01-d2dcb2fea4be_dna_r10.4.1_e8.2_5khz_400bps_hac@v4.2.0"
  [W::cram_encode_aux] Missing @RG header for RG "55d1fcf2-75f2-43b3-bd01-d2dcb2fea4be_dna_r10.4.1_e8.2_5khz_400bps_hac@v4.2.0"
  [W::cram_encode_aux] Missing @RG header for RG "55d1fcf2-75f2-43b3-bd01-d2dcb2fea4be_dna_r10.4.1_e8.2_5khz_400bps_hac@v4.2.0"
  [W::cram_encode_aux] Missing @RG header for RG "55d1fcf2-75f2-43b3-bd01-d2dcb2fea4be_dna_r10.4.1_e8.2_5khz_400bps_hac@v4.2.0"
  [W::cram_encode_aux] Missing @RG header for RG "55d1fcf2-75f2-43b3-bd01-d2dcb2fea4be_dna_r10.4.1_e8.2_5khz_400bps_hac@v4.2.0"
  [W::cram_encode_aux] Missing @RG header for RG "55d1fcf2-75f2-43b3-bd01-d2dcb2fea4be_dna_r10.4.1_e8.2_5khz_400bps_hac@v4.2.0"
  [W::cram_encode_aux] Missing @RG header for RG "55d1fcf2-75f2-43b3-bd01-d2dcb2fea4be_dna_r10.4.1_e8.2_5khz_400bps_hac@v4.2.0"
  [W::cram_encode_aux] Missing @RG header for RG "55d1fcf2-75f2-43b3-bd01-d2dcb2fea4be_dna_r10.4.1_e8.2_5khz_400bps_hac@v4.2.0"
  [W::cram_encode_aux] Missing @RG header for RG "55d1fcf2-75f2-43b3-bd01-d2dcb2fea4be_dna_r10.4.1_e8.2_5khz_400bps_hac@v4.2.0"
  [W::cram_encode_aux] Missing @RG header for RG "55d1fcf2-75f2-43b3-bd01-d2dcb2fea4be_dna_r10.4.1_e8.2_5khz_400bps_hac@v4.2.0"
  [W::cram_encode_aux] Missing @RG header for RG "55d1fcf2-75f2-43b3-bd01-d2dcb2fea4be_dna_r10.4.1_e8.2_5khz_400bps_hac@v4.2.0"
  [W::cram_encode_aux] Missing @RG header for RG "55d1fcf2-75f2-43b3-bd01-d2dcb2fea4be_dna_r10.4.1_e8.2_5khz_400bps_hac@v4.2.0"
  [W::cram_encode_aux] Missing @RG header for RG "55d1fcf2-75f2-43b3-bd01-d2dcb2fea4be_dna_r10.4.1_e8.2_5khz_400bps_hac@v4.2.0"
  [W::cram_encode_aux] Missing @RG header for RG "55d1fcf2-75f2-43b3-bd01-d2dcb2fea4be_dna_r10.4.1_e8.2_5khz_400bps_hac@v4.2.0"
  [W::cram_encode_aux] Missing @RG header for RG "55d1fcf2-75f2-43b3-bd01-d2dcb2fea4be_dna_r10.4.1_e8.2_5khz_400bps_hac@v4.2.0"
  [W::cram_encode_aux] Missing @RG header for RG "55d1fcf2-75f2-43b3-bd01-d2dcb2fea4be_dna_r10.4.1_e8.2_5khz_400bps_hac@v4.2.0"
  [W::cram_encode_aux] Missing @RG header for RG "55d1fcf2-75f2-43b3-bd01-d2dcb2fea4be_dna_r10.4.1_e8.2_5khz_400bps_hac@v4.2.0"
  [W::cram_encode_aux] Missing @RG header for RG "55d1fcf2-75f2-43b3-bd01-d2dcb2fea4be_dna_r10.4.1_e8.2_5khz_400bps_hac@v4.2.0"
  samtools view: error closing "GP004.haplotagged.cram##idx##GP004.haplotagged.cram.crai": -1

Work dir:
  /mnt/h700/omixlab/workflows/alyazeedit/Talals_analyses/Arab_ont/work/2f/2c14cc2d9a592fe71b7a07539ca7c2

Container:
  /mnt/h700/omixlab/workflows/alyazeedit/tmp/ontresearch-wf-human-variation-snp-sha17e686336bf6305f9c90b36bc52ff9dd1fa73ee9.img

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

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

Application activity log entry

No response

Were you able to successfully run the latest version of the workflow with the demo data?

yes

Other demo data information

No response