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.