Hello.

I got this error for one of 16 files. The other 15 files ran fine.

I read somewhere that this error can be a result of using single-end files instead of paired-end. The solution was to use the "contig-100.fa" file instead of the scaffold file. Since the file in my case is paired-end, I'm not sure this solution is relevant.

The script is

#!/bin/bash
#PBS -q name
#PBS -N IDBA_ud
#PBS -e error/path/IDBA_ud.ER
#PBS -o /output/path/IDBA_ud.OU
#PBS -l nodes=compute-0-311:ppn=2,mem=40gb

module load idba

file="input.fastq"
idba_ud -r "$file" -o "${file%.fastq}"

The error is

/var/spool/pbs/mom_priv/jobs/id: line 11: 27556 Segmentation fault idba_ud -r "$file" -o "${file%.fastq}"

I'd love to hear some opinions. Thanks.