"Missing @RG header" at step "snp:cat_haplotagged_contigs"

[stfacc]

Operating System

Ubuntu 22.04

Other Linux

No response

Workflow Version

v2.4.1-g64fe2fb

Workflow Execution

Command line (Local)

Other workflow execution

No response

EPI2ME Version

No response

CLI command run

BAM="/path/to/sample/bam_pass"
REF="GCA_000001405.15_GRCh38_no_alt_analysis_set.fna"

nextflow run epi2me-labs/wf-human-variation
--bam $BAM
--ref $REF
--sample_name "sample_TK2"
--snp
--sv
--cnv
--str
--phased
--threads 64

Workflow Execution - CLI Execution Profile

standard (default)

What happened?

Got an error at step "snp:cat_haplotagged_contigs"

.nextflow.log

Relevant log output

Full log is attached in previous form

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

[SamStudio8]

Hi @stfacc - these RG warnings are a red herring. The actual problem appears to be the process was killed:

  .command.sh: line 25:   145 Broken pipe             samtools cat -b cat.fofn --no-PG -o -
         146 Killed                  | samtools view --no-PG -@ 3 --reference GCA_000001405.15_GRCh38_no_alt_analysis_set.fna -O CRAM --write-index -o "sample_TK2.haplotagged.cram##idx##sample_TK2.haplotagged.cram.crai"

You can try running the workflow again, or using process selectors to increase the memory allocated to this process.

[stfacc]

Thanks for looking into this issue.

I'll check what the process selector is, and how to increase the memory, but I'm not sure I understand what's going on: samtools cat and samtools view should be streaming processes and not require much memory?