Sanity check failed by "filter_away_subset.py"

[unique379r]

Hi
All steps before "Filter away 5' degraded isoforms" were good, NO Error was reported but this script generates NO OUTPUT but just these stdout:

filter_away_subset.py testSample.collapsed

The number of PBID records in the files disagree! Sanity check failed.
# of PBIDs in testSample.collapsed.rep.fq: 660
# of PBIDs in testSample.collapsed.gff: 660
# of PBIDs in testSample.collapsed.abundance.txt: 658

I was suspecting that it might be because i used "--dun-merge-5-shorter" option in collapse_isoforms_by_sam.py but thats not the case.

Note:

1. I had used uLTRA aligment on HQ reads generated by isoseq3.
2. fusion_finder.py does not support BAM file just SAM, can you update it as collapse_isoforms_by_sam.py does supports BAM with -b.

Please help!

Thanks
Rupesh Kesharwani