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ablab / IsoQuant

Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)
https://ablab.github.io/IsoQuant/
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Issues in KeyError: 'novel' #245

Open kerrwelton opened 1 month ago

kerrwelton commented 1 month ago

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 commented 1 month ago

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 commented 1 month ago

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

andrewprzh commented 1 month ago

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

kerrwelton commented 1 month ago

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. :) :)