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Monopogen.py somatic error #101

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WeiZhaoLuck opened this issue Jan 8, 2025 · 0 comments
Open

Monopogen.py somatic error #101

WeiZhaoLuck opened this issue Jan 8, 2025 · 0 comments

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@WeiZhaoLuck
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After preProcess and germline;
An error occurred after running this command:
python app/Monopogen/src/Monopogen.py somatic
-a app/Monopogen/apps -r GRCh38.region.lst -t 10
-i out -l cell_reads_counts.csv -s featureInfo
-g genome.fa

Error:
Traceback (most recent call last):
File "/p300s/biosoft/app/Monopogen/src/Monopogen.py", line 435, in
main()
File "/p300s/biosoft/app/Monopogen/src/Monopogen.py", line 428, in main
args.func(args)
File "/p300s/biosoft/app/Monopogen/src/Monopogen.py", line 125, in somatic
validate_user_setting_somatic(args)
File "/p300s/biosoft/app/Monopogen/src/somatic.py", line 58, in validate_user_setting_somatic
logger.error("Only the whole chromsome calling is allowed!")
NameError: name 'logger' is not defined

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