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WGLab / LIQA

Long-read Isoform Quantification and Analysis
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ValueError: invalid coordinates: start (10589) > stop (9435) #6

Closed hmutpw closed 2 years ago

hmutpw commented 3 years ago

The refgene file has an error with chromosome start and end, for example: Vmn2r122 JH584292.1 + 10589 9435 ENSMUST00000178970.7,ENSMUST00000096791.11,ENSMUST00000099422.4,ENSMUST00000179115.1,ENSMUST00000071277.13,

huyustats commented 3 years ago

Hi,

I think this was caused by error in the GTF file. LIQA will eliminate this gene when doing analysis.

Y0NEKO commented 2 years ago

Hi,

I think this was caused by error in the GTF file. LIQA will eliminate this gene when doing analysis.

Hi, I had a same error when quantifying

Traceback (most recent call last):
  File "/lustre/home/acct-medsjf/medsjf-user1/.local/lib/python3.9/site-packages/liqa_src/quantify.py", line 153, in <module>
    for read in bamFilePysam.fetch(geneChr, geneStart, geneEnd):
  File "pysam/libcalignmentfile.pyx", line 1082, in pysam.libcalignmentfile.AlignmentFile.fetch
  File "pysam/libchtslib.pyx", line 688, in pysam.libchtslib.HTSFile.parse_region
ValueError: invalid coordinates: start (100003847) > stop (99995921)

What could be the reason?

rsalz commented 2 years ago

I am having the same issue with '-task quantify'. I am using a matching genome/annotation file, and i even re-aligned to be completely sure the error wasn't from my side. I get:

Traceback (most recent call last):
  File "/home/renees/anaconda3/envs/swanvis/lib/python3.7/site-packages/liqa_src/quantify.py", line 153, in <module>
    for read in bamFilePysam.fetch(geneChr, geneStart, geneEnd):
  File "pysam/libcalignmentfile.pyx", line 1082, in pysam.libcalignmentfile.AlignmentFile.fetch
  File "pysam/libchtslib.pyx", line 688, in pysam.libchtslib.HTSFile.parse_region
ValueError: invalid coordinates: start (10004092) > stop (9997331)
huyustats commented 2 years ago

Thank you for your comments! This bug has been fixed.