module load MITObim/1.9.1
MITObim.pl --help

#!/bin/bash
#$ -N MITObim
#$ -cwd
#$ -pe *mpi 4

module load MIRA/V5rc2
module load MITObim/1.9.1


mkdir tutorial1
cd tutorial1

ln -sf /apps/MITObim/1.9.1/testdata1/Tthymallus-150bp-300sd50-interleaved.fastq reads.fastq
ln -sf /apps/MITObim/1.9.1/testdata1/Salpinus-mt-genome-NC_000861.fasta reference.fa

echo -e "\n#manifest file for basic mapping assembly with illumina data using MIRA 4\n\nproject = initial-mapping-testpool-to-Salpinus-mt\n\njob=genome,mapping,accurate\n\nparameters = -NW:mrnl=0 -AS:nop=1 SOLEXA_SETTINGS -CO:msr=no\n\nreadgroup\nis_reference\ndata = reference.fa\nstrain = Salpinus-mt-genome\n\nreadgroup = reads\ndata = reads.fastq\ntechnology = solexa\nstrain = testpool\n" > manifest.conf

mira manifest.conf

ls -hlrt
ls -hlrt initial-mapping-testpool-to-Salpinus-mt_assembly/

MITObim.pl -start 1 -end 10 -sample testpool -ref Salpinus_mt_genome -readpool reads.fastq -maf initial-mapping-testpool-to-Salpinus-mt_assembly/initial-mapping-testpool-to-Salpinus-mt_d_results/initial-mapping-testpool-to-Salpinus-mt_out.maf &> log

tail log

ls -hlrt iteration1/
less iteration8/testpool-Salpinus_mt_genome_assembly/testpool-Salpinus_mt_genome_d_results/testpool-Salpinus_mt_genome_out.unpadded.fasta