Closed sabackman closed 2 months ago
RenzoTale88
commented
3 months ago Hi @sabackman thank you for opening a new issue with this and providing all the details. I can see you are running with a custom profile, would you mind confirming whether you are running in docker/singularity mode, and with which containers?
Andrea
sabackman
commented
3 months ago I'm running in singularity mode.
The container images were built using the following commands:
singularity build modkit.img docker://ontresearch/modkit:shae137452eb41f5f12b790774cafe15bc97f48d4d0
singularity build wf-common.img docker://ontresearch/wf-common:shad399cf22079b5b153920ac39ee40095a677933f1
singularity build wf-somatic-variation.img docker://ontresearch/wf-somatic-variation:sha18cc2ea1fae27fc772e7b728957996119c1ec81a
singularity build clairs-to.img docker://ontresearch/clairs-to:sha0bed006dfad374401e9410b44d67e6609f7936e9
singularity build wf-somatic-snp.img docker://ontresearch/wf-somatic-snp:sha86599ecdb46472d01e0b7c2704683f6aee8a82dd
singularity build dss.img docker://ontresearch/dss:sha28cc44cacad092f1b074aca3548ff8ba9b483fc0
singularity build wf-somatic-sv.img docker://ontresearch/wf-somatic-sv:shaf318a490c2625b8b8e4f2bc70b4dc546ce2d5ffc
singularity build snpeff.img docker://ontresearch/snpeff:sha313729d816872d70b410752001a0e2654eb88807I can see where the issue is, apologies for not spotting this immediately. The two models, while being the same, they have slightly different naming:
dna_r10.4.1_e8.2_5khz_400bps_sup@v4.2.0
dna_r10.4.1_e8.2_400bps_sup@v4.2.0Which tricks the workflow into thinking something is off. We had a similar issue in the past in wf-human-variation.
I'll open a ticket to add this model to the list of acceptable models for the next release, apologies for the inconvenience.
RenzoTale88
commented
2 months ago @sabackman we just released v1.4.0 that should address your issue. Now --override_basecaller_cfg will enforce the same basecaller model even if the two BAM have been basecalled with different models.
To update simply run:
nextflow pull epi2me-labs/wf-somatic-variation -r v1.4.0I'll close this, but please re-open if you still come across issues.
Andrea
Operating System
Centos-7
Other Linux
No response
Workflow Version
v1.3.1
Workflow Execution
CLI Cluster
Other workflow execution
No response
EPI2ME Version
No response
CLI command run
nextflow run /proj/sens2023615/wf-somatic-variation-1.3.1 \ --bam_normal /path/to/normal.bam \ --bam_tumor /path/to/tumor.bam \ --ref /path/to/genome.fa \ --sv --snv --mod --sample_name SAMPLENAME \ --override_basecaller_cfg dna_r10.4.1_e8.2_400bps_sup@v4.2.0 \ --qv 20 \ --ubam_map_threads 12 \ --normal_min_coverage 0 \ --tumor_min_coverage 0 \ -profile samuel -resume
Workflow Execution - CLI Execution Profile
None
What happened?
I'm able to successfully run the workflow on some of my samples. For other samples, multiple basecaller models are detected, distinguished only by a suffix. An error is called, and the execution halted.
Relevant log output
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