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pipeline_from_gtdbtk.sh
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pipeline_from_gtdbtk.sh
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#!/bin/sh
#SBATCH --time=100:00:00
#SBATCH --partition=largemem_q
#SBATCH -N 1
#SBATCH --mem=250G
#SBATCH --account=computeomics
echo $1 ##prefix of files
cd ${1}_bins_dir
var=( $(ls) )
echo ${var[0]}
cd ..
filename=$(basename -- "${var[0]}")
extension="${filename##*.}"
##gtdb-toolkit
gtdbtk classify_wf --genome_dir ${1}_bins_dir -x $extension --out_dir ${1}_gtdbtk_out --cpus 16
echo "gtdb-tookit done"
##MetaCHIP
MetaCHIP PI -p $1 -r c -t 6 -i ${1}_bins_dir -x $extension -taxon ${1}_gtdbtk_out/gtdbtk.bac120.summary.tsv
MetaCHIP BP -p $1 -r c -t 6
echo "MetaCHIP done"
##DIAMOND
diamond blastx -q ${1}_MetaCHIP_wd/${1}_HGT_*/${1}*BM_nc.fasta -d reference_ARG -o ${1}_diamond_out_default_ARGDB.tsv
diamond blastx -q ${1}_MetaCHIP_wd/${1}_HGT_*/${1}*BM_nc.fasta -d reference_CARD -o ${1}_diamond_out_default_CARD.tsv
echo "DIAMOND done"
##cross-checking
python3 cross_checking.py ${1}_MetaCHIP_wd/${1}_HGT_*/${1}_c_detected_HGTs.txt ${1}_diamond_out_default_ARGDB.tsv ${1}_HTARGs_ARGDB.csv
python3 cross_checking.py ${1}_MetaCHIP_wd/${1}_HGT_*/${1}_c_detected_HGTs.txt ${1}_diamond_out_default_CARD.tsv ${1}_HTARGs_CARD.csv
echo "cross-checking done"
echo "pipeline ends"