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Fast and frugal disk based k-mer counter
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KMC yields an error on fixed width fasta files #214

Open mesti90 opened 1 year ago

mesti90 commented 1 year ago

I tried to run kmc (version 3.2.2) on fasta files downloaded from the NCBI ftp server. The program gave only the following error message: Error: unknown exception

After many hours I tried to change the fasta file from fixed width to one-line sequence format, and kmc finally worked. Please add (1) a meaningful error message (2) support for fixed width fasta files

marekkokot commented 1 year ago

Hi, thank you. The error message should definitely be more informative. I think I have a fix for this, but this is not in the public version yet. fixed-width fasta (or multif-asta) is handled in kmc with -fm switch. I guess you were using -fa. If no, please let me know what was your input file and the exact command line to run KMC. Thanks again for reporting this and using KMC!

mesti90 commented 1 year ago

@marekkokot Thank you for your quick answer. I used the -fa switch, thanks for the info.

marekkokot commented 1 year ago

Great, thanks. I will keep this issue opened until I fix the error message.

yeeus commented 9 months ago

I also encountered this problem and after using -fm it's cool to get the right result