[Bug]: Error executing process > 'alignment_stats:makeQCreport (1)

[myxotheles]

What happened?

Hey guys, I tried running the wf again, having switched off SV because this seemed to crash (https://github.com/epi2me-labs/wf-somatic-variation/issues/2

This time the workflow ran far longer, about 7hrs but then crashed when making the QC report.

Few infos about my samples: 1) I am running tumour normal pair, with cell free DNA as tumour sample. Lots of short reads. Basecalled with dorado 0.3.0 duplex hac. 2) Normal control was sequenced on illumina. Not sure if this makes any difference. 3) I am running this on epi2me labs on Mac book with M2 pro and I switched on Rosetta emulation in docker.

I am hoping you can help, really keen to get this working!

Operating System

macOS

Workflow Execution

EPI2ME Labs desktop application

Workflow Execution - EPI2ME Labs Versions

Version 5.0.2 (5.0.2)

Workflow Execution - CLI Execution Profile

Docker

Workflow Version

v0.2.0

Relevant log output

Workflow execution completed unsuccessfully!
The exit status of the task that caused the workflow execution to fail was: 137.

The full error message was:

Error executing process > 'alignment_stats:makeQCreport (1)'

Caused by:
  Process `alignment_stats:makeQCreport (1)` terminated with an error exit status (137)

Command executed:

  workflow-glue report_qc \
      --window_size 50000 \
      --tumor_cov_threshold 1 \
      --normal_cov_threshold 1 \
      --sample_id SAMPLE \
      --name SAMPLE.wf-somatic-variation-readQC \
      --read_stats_normal readstats_normal.tsv.gz \
      --read_stats_tumor readstats_tumor.tsv.gz \
      --flagstat_tumor flagstat_tumor.tsv \
      --flagstat_normal flagstat_normal.tsv \
      --mosdepth_summary_tumor summary_depth_tumor.tsv \
      --mosdepth_summary_normal summary_depth_normal.tsv \
      --depth_tumor depth_tumor.tsv.gz \
      --depth_normal depth_normal.tsv.gz \
      --reference_fai ref.fa.fai \
      --versions versions.txt \
      --params params.json

Command exit status:
  137

Command output:
  (empty)

Command error:
  WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested
  /home/epi2melabs/conda/lib/python3.8/site-packages/bokeh/core/property/primitive.py:37: DeprecationWarning: `np.bool8` is a deprecated alias for `np.bool_`.  (Deprecated NumPy 1.24)
    bokeh_bool_types += (np.bool8,)
  [23:15:42 - workflow_glue] Starting entrypoint.
  [23:15:43 - workflow_glue.report_qc ] Loading ref.fa.fai
  [23:15:43 - workflow_glue.report_qc ] Loading readstats_tumor.tsv.gz
  [23:17:36 - workflow_glue.report_qc ] Loading readstats_normal.tsv.gz
  .command.sh: line 18:    31 Killed                  workflow-glue report_qc --window_size 50000 --tumor_cov_threshold 1 --normal_cov_threshold 1 --sample_id SAMPLE --name SAMPLE.wf-somatic-variation-readQC --read_stats_normal readstats_normal.tsv.gz --read_stats_tumor readstats_tumor.tsv.gz --flagstat_tumor flagstat_tumor.tsv --flagstat_normal flagstat_normal.tsv --mosdepth_summary_tumor summary_depth_tumor.tsv --mosdepth_summary_normal summary_depth_normal.tsv --depth_tumor depth_tumor.tsv.gz --depth_normal depth_normal.tsv.gz --reference_fai ref.fa.fai --versions versions.txt --params params.json

Work dir:
  /Users/thomaserblich/epi2melabs/instances/wf-somatic-variation_9058921c-2d57-4c27-9f39-638d01b292f2/work/0c/52720a580b2f9f85d6a3fa73f54d50

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

[myxotheles]

I could reproduce the same error running it on our Linux CentOS cluster.

[myxotheles]

I could resolve this issue by allocating more memory. Now running with 16 cores and 3GB/core seems to be working.