pycoqc not working

Hello,
I searched and couldn’t find any other info about this, so I’ll post for help. I’m trying to run pycoqc and it’s returning an error, the last few lines of which are:

packages/pycoQC/pycoQC_parse.py", line 89, in init
self.bam_file_list = expand_file_names(bam_file, bam_check=True)
File “/usr/local/tools/_conda/envs/__pycoqc@2.5.2/lib/python3.7/site-packages/pycoQC/common.py”, line 339, in expand_file_names
with ps.AlignmentFile(f, “rb”) as bam:
File “pysam/libcalignmentfile.pyx”, line 741, in pysam.libcalignmentfile.AlignmentFile.cinit
File “pysam/libcalignmentfile.pyx”, line 990, in pysam.libcalignmentfile.AlignmentFile._open
ValueError: file has no sequences defined (mode=‘rb’) - is it SAM/BAM format? Consider opening with check_sq=False

The tool used to work, and I reran it with data from several months ago that worked previously but got this error today. Is the tool still available? Thanks.

Hi @lkothera

What Galaxy server do you use? I don’t see any issue with Pycoqc on Galaxy Australia.

Have you tested the tool with a known dataset? Try this:

Does it work on the tutorial data?

The error message suggests it might be the data (file has no sequences defined ).

Kind regards,
Igor

Hi Igor, I got it to work if I choose to only have it use the .tsv file generated by Dorado, and not include the optional BAM file. So it appears to be working. Thank you for the reply.