error while creating kover dataset from fastq

Question

[ekaterina.avershina]

I am using Kover (https://github.com/aldro61/kover) to predict AR in Klebsiella. The program fails while creating the .kover dataset from the list of my fastqfiles. The command starts running, gets through 40 - 50 % and quits.

what i do:

kover dataset create from-reads --genomic-data $mypath/genomes.tsv --phenotype-metadata $mypath/metadata.tsv --phenotype-description $description --output $mypath/out --kmer-size 31 --kmer-min-abundance 3 --n-cpu 0 -x

the output i get is:

EXCEPTION: Kmer solidity has more thresholds (1) than banks (0)54 %

How do i fix this? Is it a problem with fastq.gz files i have?

Answer 1

[Alexandre Drouin]

Sorry for the late reply. It's the first time that I see this exception come out of DSK (the k-mer counter used by kover). Could you please show me a few lines of genomes.tsv and metadata.tsv? If you're able to share one of your fastq.gz files it would also be very useful.

Thanks! Alex