I'm trying to run DiscoSNP++ on data from the Tara Oceans Expedition but I ran into a problem that i have trouble solving. The input I'm using are two very large .gz files (study accession PRJEB4352). The output that I need are a .fa file and a .vcf file, but those don't show up. This is the script I used for the job which took about 40 minutes to complete:
#!/usr/bin/env bash #PBS -l nodes=1:ppn=1 #PBS -l walltime=02:00:00 #PBS -l pmem=8gb #PBS -A default_project cd /vsc-hard-mounts/leuven-data/341/vsc34135/Laso-Jadart source /vsc-hard-mounts/leuven-data/341/vsc34135/miniconda3/etc/profile.d/conda.sh conda activate discosnp_env curl -o ERR868369_1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR868/ERR868369/ERR868369_1.fastq.gz curl -o ERR868369_2.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR868/ERR868369/ERR868369_2.fastq.gz run_discoSnp++.sh -r fof_1.txt –k 51 -b 1 -T
With fof_1.txt being: ERR868369_1.fastq.gz ERR868369_2.fastq.gz
This is part of the error job output
And this is part of the job output:
I'm quite new to making scripts and working with the VSC so any help is appreciated.