kneaddata做质控的时候，服务器卡死了，用trimmomatic+bowtie2分开跑是可以的吧

tail -n+2 $datafile/metadata_WBBW_all.txt | cut -f1 | rush -j 4 'java -jar /share/work/biosoft/Trimmomatic/Trimmomatic-0.39/trimmomatic-0.39.jar PE \

-threads 6 \

"$datafile"/{}_1.fq.gz "$datafile"/{}_2.fq.gz \

"$workdir"/1.host_del_and_qc/kneaddata/{}_forward_paired.fq.gz "$workdir"/1.host_del_and_qc/kneaddata/{}_forward_unpaired.fq.gz \

"$workdir"/1.host_del_and_qc/kneaddata/{}_reverse_paired.fq.gz "$workdir"/1.host_del_and_qc/kneaddata/{}_reverse_unpaired.fq.gz \

ILLUMINACLIP:/share/work/biosoft/Trimmomatic/Trimmomatic-0.39/adapters/TruSeq3-PE.fa:2:40:15 \

LEADING:3 TRAILING:3 SLIDINGWINDOW:50:20 MINLEN:120' 这个是trimmomatic修剪质控的代码再加上1.host_del_and_qc.sh中fastp质控后，bowtie2去宿主的代码进行质控和去宿主的操作是没问题的吧

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