samcomp

[rezarahman12]

Describe the bug

Dear Nanocomopore team (@lmulroney),

Thank you for this very useful software. This is not an issue rather help is needed to run the nanocompore's sampcomp.

My script is given below:

!/bin/bash

PBS -A UQ-QBI

PBS -l select=1:ncpus=22:mem=120GB

PBS -e /scratch/project_mnt/S0077/xPore/rawdata/xpore_data/nanocompore/sampcom_allrep

PBS -o /scratch/project_mnt/S0077/xPore/rawdata/xpore_data/nanocompore/sampcom_allrep

PBS -l walltime=24:00:00

PBS -N allrepsampcomp

cd $PBS_O_WORKDIR

module load nanocompore/1.0.4

dir=/scratch/project_mnt/S0077/xPore/rawdata/xpore_data

input=${dir}/nanocompore

wt1=${input}/wt-rep1/out/out_eventalign_collapse.tsv wt2=${input}/wt-rep2/out/out_eventalign_collapse.tsv wt3=${input}/wt-rep3/out/out_eventalign_collapse.tsv ko1=${input}/ko-rep1/out/out_eventalign_collapse.tsv ko2=${input}/ko-rep2/out/out_eventalign_collapse.tsv ko3=${input}/ko-rep3/out/out_eventalign_collapse.tsv

output=${dir}/nanocompore/sampcom_allrep

nanocompore sampcomp --min_coverage 30 --downsample_high_coverage 1000 --overwrite --nthreads 22 \ --file_list1 ${wt1}, ${wt2}, ${wt3} \ --file_list2 ${ko1}, ${ko2}, ${ko3} \ --label1 wt \ --label2 ko \ --fasta /scratch/project_mnt/S0077/xPore/Homo_sapiens.GRCh38.cdna.all.fa \ --outpath ${output}

The error I am getting is given below:

usage: nanocompore [-h] [--version] {sampcomp,simreads,eventalign_collapse} ... nanocompore: error: unrecognized arguments: /scratch/project_mnt/S0077/xPore/rawdata/xpore_data/nanocompore/wt-rep2/out/out_eventalign_collapse.tsv, /scratch/project_mnt/S0077/xPore/rawdata/xpore_data/nanocompore/wt-rep3/out/out_eventalign_collapse.tsv /scratch/project_mnt/S0077/xPore/rawdata/xpore_data/nanocompore/ko-rep2/out/out_eventalign_collapse.tsv, /scratch/project_mnt/S0077/xPore/rawdata/xpore_data/nanocompore/ko-rep3/out/out_eventalign_collapse.tsv

When I use one replicate per condition then it works, but when multiple replicates are given as above it says unrecognized arguments. Could you please help me to fix the issue? I do highly appreciate your time and help.

Kind regards Reza