IndexError: list index out of range

[creaturemoon]

Hello,
I processed pacbio ccs reads using IsoQuant v3.4.0 with standard reference. In the log file, the error occured with "IndexError: list index out of range. ". Here is the log, isoquant.log. The command is

isoquant.py -d pacbio_ccs -r Drosophila_melanogaster.BDGP6.32.dna.toplevel.fa -g Drosophila_melanogaster.BDGP6.32.52.gtf --complete_genedb --bam sample1.bam sample2.bam -l sample1 sample2 --report_novel_unspliced true -o ./output -t 40 --polya_requirement never

I ran the same samples and command (without --polya_requirement never) using v3.3.1 and there was no such error. Do you know about this? Additionally, there was a warning although I used --polya_requirement never in v3.4.0, so I was confused whether it had worked.

WARNING` - PolyA percentage is suspiciously low. IsoQuant expects non-polya-trimmed reads. If you aim to construct transcript models, consider using --polya_requirement option.

Looking forward to your reply.
Thank you.

[andrewprzh]

Dear @creaturemoon

Thanks for the report!

I think I found and fixed the bug, so I'll make a 3.4.1 release soon. If you download IsoQuant yourself (and not via conda), I can provide you a patch now. If not, bug-fix release will be out in a few hours once testing is done.

With respect to the warning - simply ignore it, it is printed by mistake. According to the log, the option worked correctly:

2024-05-09 21:13:57,909 - INFO -   Novel monoexonic transcripts will be reported: yes
2024-05-09 21:13:57,909 - INFO -   PolyA tails are required for multi-exon transcripts to be reported: no
2024-05-09 21:13:57,909 - INFO -   PolyA tails are required for 2-exon transcripts to be reported: no
2024-05-09 21:13:57,909 - INFO -   PolyA tails are required for known monoexon transcripts to be reported: no
2024-05-09 21:13:57,909 - INFO -   PolyA tails are required for novel monoexon transcripts to be reported: yes

However, novel mono-exonic transcript can now be only reported with polyA tails (this is how the algorithm is designed and there is now way to easily change it). Thus, you may get better results if you manage to keep polyA tails.
In the future we plan to support PacBio CCS headers that contain information about polyA-tail trimming.

Best
Andrey

[andrewprzh]

Should be fixed in https://github.com/ablab/IsoQuant/releases/tag/v3.4.1

[creaturemoon]

Hello,
I got it. Thank you so much.