Open lucy924 opened 2 weeks ago
Hi @lucy924 would it be possibly for you to share the content of the files in:
/weka/dejlu879/BEBIC/CellLineB/wf-sv_B3_CvT/chr1/work/b8/e5f19b20c7843b5522c1ae7f8aff58/tumor_summary/
Thanks in advance Andrea
Sure tumor_summary.gz
Operating System
Ubuntu 22.04
Other Linux
No response
Workflow Version
v1.3.1
Workflow Execution
Command line (Cluster)
Other workflow execution
No response
EPI2ME Version
No response
CLI command run
nextflow run epi2me-labs/wf-somatic-variation -params-file params_weka.json -c custom.config -profile singularity -resume
params_weka.json
Workflow Execution - CLI Execution Profile
singularity
What happened?
I'm slowly ironing out all the issues in this test run with one pair of samples on chr1, and the latest issue appears to be in the below section of code according to the error: https://github.com/epi2me-labs/wf-somatic-variation/blob/ba53c64fc63127ffd9ead61e1cc1946557238aae/bin/workflow_glue/report_mod.py#L205
I ran it successfully on the demo data but the demo data run didn't do most of the tumour processing which appears to be the problem here.
Thanks!
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
No response