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Unable to run #5

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dfermin opened this issue Dec 12, 2022 · 0 comments
Open

Unable to run #5

dfermin opened this issue Dec 12, 2022 · 0 comments

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@dfermin
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dfermin commented Dec 12, 2022

Hello.
I'm trying to run SPLICE-q on one of my samples but it continues to crash.
The command I execute is:

SPLICE-q.py -g ../conf/human.GRCh38.ensembl_rel107.gtf -b sample_001.bam -p 8 -o sample_001.txt

This is the output I get:

(py36) [dfermin@Lnx67 SPLICE-q]$ SPLICE-q.py -g ../conf/human.GRCh38.ensembl_rel107.gtf -b sample_001.bam -p 8 -o sample_001.txt
Index available
12/12/22   14:33   Parsing splice junctions...
Traceback (most recent call last):
  File "/home/dfermin/miniconda3/envs/biopy/bin/SPLICE-q.py", line 776, in <module>
    main()
  File "/home/dfermin/miniconda3/envs/biopy/bin/SPLICE-q.py", line 510, in main
    main_nocoverage(parser)
  File "/home/dfermin/miniconda3/envs/biopy/bin/SPLICE-q.py", line 543, in main_nocoverage
    bam = pysam.AlignmentFile(bamfile, 'rb')
  File "pysam/calignmentfile.pyx", line 311, in pysam.calignmentfile.AlignmentFile.__cinit__ (pysam/calignmentfile.c:4929)
  File "pysam/calignmentfile.pyx", line 393, in pysam.calignmentfile.AlignmentFile._open (pysam/calignmentfile.c:6013)
  File "pysam/calignmentfile.pyx", line 60, in pysam.calignmentfile._encodeFilename (pysam/calignmentfile.c:3593)
TypeError: Argument must be string or unicode.

I have verified that my input files are not corrupt.
Any suggestions what might be wrong?
Thanks

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