run_WGS.bowtie2.minikraken-pipeline

inputpath=/data/lijing/data
outputpath=/data/lijing/test

cd $inputpath
ls *.gz|awk '{split($0,a,"_");print a[1]"_"a[2]"_"a[3]}' |sort|uniq > ${outputpath}/name.uniq.txt

for j in `cat ${outputpath}/name.uniq.txt`
do
java -jar /home/biosoft/Trimmomatic-0.38/trimmomatic-0.38.jar PE \
        -threads 30 -phred33 \
        -trimlog ${outputpath}/${j}.trim.log \
        ${inputpath}/${j}_R1_001.fastq.gz ${inputpath}/${j}_R2_001.fastq.gz \
        ${outputpath}/${j}.r1.paired.fq.gz ${outputpath}/${j}.r1.unpaired.fq.gz ${outputpath}/${j}.r2.paired.fq.gz ${outputpath}/${j}.r2.unpaired.fq.gz \
        MINLEN:150 AVGQUAL:30
done

for j in `cat ${outputpath}/name.uniq.txt`
do
/home/biosoft/bowtie2-2.3.5.1/bowtie2 \
        -p 20 -x /data/database/hg38/hg38_bowtie2/hg38 \
        -1 ${outputpath}/${j}.r1.paired.fq.gz \
        -2 ${outputpath}/${j}.r2.paired.fq.gz \
        -S ${outputpath}/${j}.sam \
        --un-conc-gz ${outputpath}/${j}.human.fq.gz
done

for j in `cat ${outputpath}/name.uniq.txt`
do
/data/lijing/download_software/kraken2/kraken2 \
        --db /data/lijing/download_software/kraken2_database/minikraken/minikraken_8GB_20200312 \
        --threads 24 \
        --minimum-hit-groups 2 \
        --report ${outputpath}/${j}.2.kreport2 \
        --paired ${outputpath}/${j}.human.fq.1.gz ${outputpath}/${j}.human.fq.2.gz > \
        ${outputpath}/${j}.2.kraken2 && \
        /usr/bin/python3 /data/lijing/test_mngs_line/20230625.classify_kraken_out.count.py \
        -i1 ${outputpath}/${j}.2.kreport2 \
        -o1 ${outputpath}/${j}.2.classify.last.xls
done

for j in `cat ${outputpath}/name.uniq.txt`
do
/data/lijing/download_software/kraken2/kraken2 \
        --db /data/lijing/download_software/kraken2_database/minikraken/minikraken_8GB_20200312 \
        --threads 24 \
        --minimum-hit-groups 5 \
        --report ${outputpath}/${j}.5.kreport2 \
        --paired ${outputpath}/${j}.human.fq.1.gz ${outputpath}/${j}.human.fq.2.gz > \
        ${outputpath}/${j}.5.kraken2 && \
        /usr/bin/python3 /data/lijing/test_mngs_line/20230625.classify_kraken_out.count.py \
        -i1 ${outputpath}/${j}.5.kreport2 \
        -o1 ${outputpath}/${j}.5.classify.last.xls
done

for j in `cat ${outputpath}/name.uniq.txt`
do
/data/lijing/download_software/kraken2/kraken2 \
        --db /data/lijing/download_software/kraken2_database/minikraken/minikraken_8GB_20200312 \
        --threads 24 \
        --minimum-hit-groups 8 \
        --report ${outputpath}/${j}.8.kreport2 \
        --paired ${outputpath}/${j}.human.fq.1.gz ${outputpath}/${j}.human.fq.2.gz > \
        ${outputpath}/${j}.8.kraken2 && \
        /usr/bin/python3 /data/lijing/test_mngs_line/20230625.classify_kraken_out.count.py \
        -i1 ${outputpath}/${j}.8.kreport2 \
        -o1 ${outputpath}/${j}.8.classify.last.xls
done

for j in `cat ${outputpath}/name.uniq.txt`
do
/data/lijing/download_software/kraken2/kraken2 \
        --db /data/lijing/download_software/kraken2_database/minikraken/minikraken_8GB_20200312 \
        --threads 24 \
        --minimum-hit-groups 10 \
        --report ${outputpath}/${j}.10.kreport2 \
        --paired ${outputpath}/${j}.human.fq.1.gz ${outputpath}/${j}.human.fq.2.gz > \
        ${outputpath}/${j}.10.kraken2 && \
        /usr/bin/python3 /data/lijing/test_mngs_line/20230625.classify_kraken_out.count.py \
        -i1 ${outputpath}/${j}.10.kreport2 \
        -o1 ${outputpath}/${j}.10.classify.last.xls
done

for j in `cat ${outputpath}/name.uniq.txt`
do
/data/lijing/download_software/kraken2/kraken2 \
        --db /data/lijing/download_software/kraken2_database/minikraken/minikraken_8GB_20200312 \
        --threads 24 \
        --minimum-hit-groups 15 \
        --report ${outputpath}/${j}.15.kreport2 \
        --paired ${outputpath}/${j}.human.fq.1.gz ${outputpath}/${j}.human.fq.2.gz > \
        ${outputpath}/${j}.15.kraken2 && \
        /usr/bin/python3 /data/lijing/test_mngs_line/20230625.classify_kraken_out.count.py \
        -i1 ${outputpath}/${j}.15.kreport2 \
        -o1 ${outputpath}/${j}.15.classify.last.xls
done

for j in `cat ${outputpath}/name.uniq.txt`
do
/data/lijing/download_software/kraken2/kraken2 \
        --db /data/lijing/download_software/kraken2_database/minikraken/minikraken_8GB_20200312 \
        --threads 24 \
        --minimum-hit-groups 20 \
        --report ${outputpath}/${j}.20.kreport2 \
        --paired ${outputpath}/${j}.human.fq.1.gz ${outputpath}/${j}.human.fq.2.gz > \
        ${outputpath}/${j}.20.kraken2 && \
        /usr/bin/python3 /data/lijing/test_mngs_line/20230625.classify_kraken_out.count.py \
        -i1 ${outputpath}/${j}.20.kreport2 \
        -o1 ${outputpath}/${j}.20.classify.last.xls
done

for j in `cat ${outputpath}/name.uniq.txt`
do
/data/lijing/download_software/kraken2/kraken2 \
        --db /data/lijing/download_software/kraken2_database/minikraken/minikraken_8GB_20200312 \
        --threads 24 \
        --minimum-hit-groups 25 \
        --report ${outputpath}/${j}.25.kreport2 \
        --paired ${outputpath}/${j}.human.fq.1.gz ${outputpath}/${j}.human.fq.2.gz > \
        ${outputpath}/${j}.25.kraken2 && \
        /usr/bin/python3 /data/lijing/test_mngs_line/20230625.classify_kraken_out.count.py \
        -i1 ${outputpath}/${j}.25.kreport2 \
        -o1 ${outputpath}/${j}.25.classify.last.xls
done

for j in `cat ${outputpath}/name.uniq.txt`
do
/data/lijing/download_software/kraken2/kraken2 \
        --db /data/lijing/download_software/kraken2_database/minikraken/minikraken_8GB_20200312 \
        --threads 24 \
        --minimum-hit-groups 30 \
        --report ${outputpath}/${j}.30.kreport2 \
        --paired ${outputpath}/${j}.human.fq.1.gz ${outputpath}/${j}.human.fq.2.gz > \
        ${outputpath}/${j}.30.kraken2 && \
        /usr/bin/python3 /data/lijing/test_mngs_line/20230625.classify_kraken_out.count.py \
        -i1 ${outputpath}/${j}.30.kreport2 \
        -o1 ${outputpath}/${j}.30.classify.last.xls
done

for j in `cat ${outputpath}/name.uniq.txt`
do
/data/lijing/download_software/kraken2/kraken2 \
        --db /data/lijing/download_software/kraken2_database/minikraken/minikraken_8GB_20200312 \
        --threads 24 \
        --minimum-hit-groups 40 \
        --report ${outputpath}/${j}.40.kreport2 \
        --paired ${outputpath}/${j}.human.fq.1.gz ${outputpath}/${j}.human.fq.2.gz > \
        ${outputpath}/${j}.40.kraken2 && \
        /usr/bin/python3 /data/lijing/test_mngs_line/20230625.classify_kraken_out.count.py \
        -i1 ${outputpath}/${j}.40.kreport2 \
        -o1 ${outputpath}/${j}.40.classify.last.xls
done