Issues in KeyError: 'novel'

[kerrwelton]

Hi, thank you for developing this excellent software. I encountered an issue while running isoquant.py to analyze Oxford Nanopore data. Could you please let me know how to resolve it? I would greatly appreciate it.

Here are the parameters I used when running isoquant.py.
isoquant.py --reference GRCh38.p14.genome.fa
--genedb gencode.v46.annotation.gtf --complete_genedb
--bam memcd4.bam ncd4.bam ncd8.bam --labels memcd4 ncd4 ncd8
--data_type nanopore
-o isoquant_result
--threads 80
--check_canonical

The error message when running isoquant.py was saved in nohup.out.log, isoquant.log is the automatically generated by isoquant.py.
isoquant.log
nohup.out.log

[andrewprzh]

Hi @kerrwelton

Thanks for the feedback! Which version are you using? It seems I've seen issue in one of the previous IsoQuant versions and had been fixed since then.

Best
Andrey

[kerrwelton]

I am using isoquant v2.2.0. Do I need to upgrade to a higher version?

[andrewprzh]

Yes, 2.2 is more than 2 years old, current version is 3.6, I highly recommend updating.

[kerrwelton]

I updated isoquant to the latest version and rerun isoquant.py. Now it runs successfully with no error message. Thanks for you rapid and helpful response. :) :)