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KCCG / ClinSV

Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data
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exist status: 256 run on cnvnator stage #41

Open OlenaMaiakovska opened 1 year ago

OlenaMaiakovska commented 1 year ago

Hi all,

I am running test dataset based on refdata-b38 and got the following error: "error exist status != 0 (256), please check /app/project_folder/SVs/FR05812606/cnvnator/sh/cnvnator.caller.FR05812606.e for more information".

The error file last lines comprise the message:
" ===== Running calls on input data Traceback (most recent call last): File "/app/clinsv/cnvnator-multi/cnvnator_wrapper.py", line 234, in mk_graph_file(args.output) File "/app/clinsv/cnvnator-multi/cnvnator_wrapper.py", line 182, in mk_graph_file start = int(pieces[1][idx+1:idx2]) ValueError: invalid literal for int() with base 10: 'o' " Can anybody help to figure out the reason? Thank you!

drmjc commented 1 year ago

thanks for reporting this Olena, this is a new one for us. What command did you run please?