NanoPlot 1.42.0 has crashed
mithunbge06 opened this issue · 2 comments
Hello Nanoplot community,
I am trying to run QC on PacBio_HiFi long read data (.bam file).
Unfortunately, NanoPlot 1.42.0 keeps crashing. I have attached the log file of the run.
There was an error "ValueError: file has no sequences defined (mode='rb') - is it SAM/BAM format? Consider opening with check_sq=False". I have tried to open it with "check_sq=False" but still getting the same error.
Pysam suggests that your data may be corrupted. Is your bam file aligned? Could you try with --ubam instead of --bam?
My data was not aligned. Also, there were some version conflicts in our HPC system. At last, I have used a virtual environment to install NanoPlot and used --ubam as you suggested. It seems to be working. Thank you.