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sanger-pathogens / iva

de novo virus assembler of Illumina paired reads
http://sanger-pathogens.github.io/iva/
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IVA: kmc error #103

Open waqasuddinkhan opened 3 years ago

waqasuddinkhan commented 3 years ago

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] Parameters:

- 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: `/home/admin1/anaconda3/bin/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 IVA 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` Any help is appreciated, Waqas.