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babelomics / ngscat2

Improved version of Next Generation Sequencing data Capture Assessment Tool (ngsCAT)
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program failed #3

Open lmanchon opened 3 years ago

lmanchon commented 3 years ago

--Hi,

runnning: ngscat2 --bams ./SRR6823381.bam --bed ./Exome-Agilent.bed --out /work/ngscat --reference ./Homo_sapiens_hg38.fasta

it failed with:

Traceback (most recent call last): File "ngscat2", line 8, in sys.exit(main()) File "main.py", line 416, in main generate_report(options, config) File "/.local/lib/python3.7/site-packages/ngscat2/main.py", line 290, in generatereport cover, = bam.myCoverageBed(options.bed, bedGraphFile=mainReporter.outdir) File "/.local/lib/python3.7/site-packages/ngscat2/misc/bam_file.py", line 518, in myCoverageBed endPositions.append(int(currentRead.aend)) TypeError: int() argument must be a string, a bytes-like object or a number, not 'NoneType'

how to identify the problem? thank you --

Alnkhife commented 2 months ago

i'm getting the same issue, any help is appreciated.

Best,