tleonardi
samcomp
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
