cnv_spectre: callCNV gets stuck

ilivyatan commented 3 months ago

Operating System

Ubuntu 22.04

Other Linux

No response

Workflow Version

11

Workflow Execution

Command line (Local)

Other workflow execution

No response

EPI2ME Version

No response

CLI command run

~/nextflow run epi2me-labs/wf-human-variation -profile standard --snp --sv --cnv --bam 20240303_1209_2B_PAO92639_a95fbad5/30169_dorado_aligned_sorted.bam --ref /data/referncess/GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fna --out_dir epi2me_out --basecaller_cfg 'dna_r10.4.1_e8.2_400bps_hac@v4.3.0' --sample_name '30169_dorado_aligned_sorted'

Workflow Execution - CLI Execution Profile

standard (default)

What happened?

The pipeline completed the snp and sv analyses, but just got stuck at the CNV analysis, which stayed at 0% (0 out of 1) for 24 hours till forced termination.

Relevant log output

I can provide trace.txt and other reports

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

TBradley27 commented 3 months ago

Hey,

This is just informal advice from another user, but try playing around with memory and/or threads allocation (as described in #65)

I had a process in another ONT workflow take >18 hours. I terminated the job, allocated a lot more memory and cpus and this particular process completed <2 hours next time I ran it

ilivyatan commented 2 months ago

Thanks for the advice, in this case it seems that the process doesn't even start.

vlshesketh commented 2 months ago

Hi @ilivyatan, please can you provide the .nextflow.log so we investigate this further?

vlshesketh commented 1 month ago

Hi @ilivyatan please can you let us know if this is still causing an issue, and send the .nextflow.log if so?

vlshesketh commented 1 month ago

HI @ilivyatan, closing this through lack of response but please re-open if you require further support.

epi2me-labs / wf-human-variation