Hi,

I tried the following command:

iva --trimmomatic trimmomatic-0.39.jar --adapters ../adapters.fasta -f ../AKULO_S1_L001_R1_001.fastq.gz -r ../AKULO_S1_L001_R2_001.fastq.gz MyOutputDirectory/ --threads 96

But came with this error:

The following command failed with exit code 1
bash run_kmc.sh

The output was:

KMC dump ver. 2.1.1 (2015-01-22)

Usage:
kmc_dump [options] <kmc_database> <output_file>
Parameters:
<kmc_database> - kmer_counter's output
Options:
-ci - print k-mers occurring less than times
-cx - print k-mers occurring more of than times

I am using UBUNTU 20.0.4. The info.txt file has:

version 1.0.8 Using kmc version 2.1.1 Using kmc_dump version 2.1.1 Using nucmer version UNKNOWN ... I tried running this to get the version: "nucmer --version" and the output didn't match this regular expression: "^NUCmer (NUCleotide MUMmer) version (.*)$" Using samtools version 1.10 Using smalt version 0.7.6

Posted the same on IVA's GitHub Page: https://github.com/sanger-pathogens/iva/issues/103

Any help is appreciated,

Waqas.