makeReport issue, docker container crash

[jh4yd]

Operating System

Ubuntu 22.04

Other Linux

No response

Workflow Version

v1.2.1

Workflow Execution

EPI2ME Desktop (Local)

Other workflow execution

No response

EPI2ME Version

v5.1.14

CLI command run

No response

Workflow Execution - CLI Execution Profile

None

What happened?

6 samples across 2 PromethION runs, as I reported earlier. This time on Ubuntu 22.04, I allocated 60 GB of memory to the makereport process, but it couldn’t complete and caused Docker to crash.

Relevant log output

[16:35:45 - workflow_glue] Bootstrapping CLI.
/home/epi2melabs/conda/lib/python3.8/site-packages/gffutils/parser.py:19: DeprecationWarning: invalid escape sequence \w
  gff3_kw_pat = re.compile('\w+=')
[16:35:53 - workflow_glue] Starting entrypoint.
/home/epi2melabs/conda/lib/python3.8/site-packages/pandas/util/_decorators.py:311: ParserWarning: Falling back to the 'python' engine because the 'c' engine does not support regex separators (separators > 1 char and different from '\s+' are interpreted as regex); you can avoid this warning by specifying engine='python'.
  return func(*args, **kwargs)
/home/epi2melabs/conda/lib/python3.8/site-packages/gffutils/create.py:724: UserWarning: It appears you have a transcript feature in your GTF file. You may want to use the `disable_infer_transcripts=True` option to speed up database creation
  warnings.warn(
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time="2024-07-19T13:26:58-04:00" level=error msg="error waiting for container: unexpected EOF"

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

[sarahjeeeze]

Hi, how large are your input samples? And are you running this on a laptop do you have plenty of disk space? How are you allocating the 60gb memory have you increase the memory available in docker settings as well as the workflow for this process? Although i would not have thought 60gb memory is required for the make report process

[jh4yd]

hi @sarahjeeeze ,
The fastq file sizes of full-length-read for these samples were about 10GB to 30 GB. The disk had plenty of space.
Docker was allocated 64GB, the process was allocated 60GB. I could see the report process used a maximum of about 35 GB. I don't think it was memory issue causing the error. As you can see the error code was not 137 but 125.

[sarahjeeeze]

Could you share the nextflow.log?

[jh4yd]

Could you share the nextflow.log?

nextflow.log

[sarahjeeeze]

in the settings of the app have you also increased the docker memory allowance to 60gb? 125 is usually the container failing to execute.

[jh4yd]

yes, we have. here's a screenshot of docker setting.

[sarahjeeeze]

We have an update coming to the workflow this Wednesday which should reduce to memory required by the report step considerably which will hopefully fix this issue.