#start interactive job
qsub -I -l walltime=4:0:0 -q default@meta-pbs.metacentrum.cz -l select=1:ncpus=8:mem=8gb:scratch_local=8gb
cd /storage/brno2/home/$LOGNAME/
cd HybSeqSource

#download script for preparing cpDNA reference
wget https://raw.githubusercontent.com/tomas-fer/scripts/master/extractGBplastome.sh
#download
wget https://raw.githubusercontent.com/tomas-fer/scripts/master/product.txt

#download GenBank file with full plastome reference in GenBank format
#e.g. Wurfbainia villosa NC044746
#https://www.ncbi.nlm.nih.gov/ - select nucleotide (not All databases), search for NC044746, click on 'Send to', select File, Format: GenBank, Create File
#rename the downloaded file to 'Wurfbainia-villosa_NC044746.gb' and upload to MetaCentrum (HybSeqSource folder)

#run the script
chmod +x extractGBplastome.sh
./extractGBplastome.sh Wurfbainia-villosa_NC044746.gb
#this create many references for HybPhyloMaker

cd ../HybPhyloMaker
#edit settings
nano settings.cfg
cp=yes
cpDNACDS=Wurfbainia-villosa_NC044746_reference_CDSnonHPM200.fasta

#run script to prepare pseudoreference
qsub HybPhyloMaker0b_preparereference.sh

#Map reads to chloroplast pseudoreference
qsub HybPhyloMaker2a_readmappingParallel.sh

#Run this submitter created by the previous job (this script submits 35 jobs)
cd HybSeqCourse2023/cp/21mapped_bwa/ && ./submitMappingJobs.sh && cd ../../..

#Run the summary script (after all jobs are finished)
qsub HybPhyloMaker2a2_readmappingParallel_summary.sh

#continue as with normal HybPhyloMaker analysis - results are now in the 'cp' folder