#!/bin/bash
#SBATCH -N 1 # Number of tasks 
#SBATCH -n 14 # All tasks on one machine 
#SBATCH -t 3-00:00:00 # walltime, abbreviated by -t
##SBATCH -p gompert-np # Partition on some cluster
##SBATCH -A gompert # General CHPC account 
#SBATCH -o mitogenomesPP.slurm.out # Standard output 
#SBATCH -e mitogenomesPP.pairs.slurm.err # Standard error
#SBATCH --mail-type=fail
#SBATCH --mail-user=vaninatonzo@gmail.com
#Load bowtie2 and samtools
module spider python/3.10.3
module load bowtie2/2-2.2.9;
module load blast/2.11.0
module load spades/3.15.4

while read T;
   do
   ./get_organelle_from_reads.py  -s liniphidae_c1_xs.fasta -1 ../../00_Trimmomatic/${T}_1_paired.fq.gz  -2 ../../00_Trimmomatic/${T}_2_paired.fq.gz  -F animal_mt -o ../../HN00176099_hdd1/mitogenomes/${T}_mitogenome -R 15 -w 95
 done < TAXA.txt