Entering edit mode
3.0 years ago
waqasnayab
▴
250
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.
