Question: error while creating kover dataset from fastq
0
gravatar for ekaterina.avershina
18 months ago by
ekaterina.avershina0 wrote:

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?

kover kmer • 405 views
ADD COMMENTlink modified 18 months ago by Alexandre Drouin60 • written 18 months ago by ekaterina.avershina0
0
gravatar for Alexandre Drouin
18 months ago by
Montreal, Canada
Alexandre Drouin60 wrote:

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

ADD COMMENTlink written 18 months ago by Alexandre Drouin60
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