文章目录

• 关于宏基因组分析
• • 什么是宏基因组分析测序？
• 准备-----宏基因组集群上需要用到的环境和工具（在服务器对测序数据进行组装和质控，排除宿主的DNA，根据OTU获取菌落的丰度的表，或者进行基因功能注释。）
• • Anaconda------类似于虚拟机，能够快速构建环境，傻瓜式--即conda命令
  • snakemake (v5.14.0)----流程控制软件，调控软件合作运行
  • python3 (v3.6.10), pandas-----生物信息分析软件底层支持
  • bowtie2 (v2.3.5.1)----序列比对软件--主要用于去除宿主的序列
  • samtools (v1.9)----一款对于bam格式文件进行赛选，排序，操作的软件，可以转换文件类型。为metaphlan3做好数据准备
  • metaphlan3 (v3.0)---根据质控数据获取物种丰度
  • seqkit (v0.12.1)
• **==__关于集群__==**
• • 关于节点篇
  • • • qstat命令内容展示
      • tail命令
      • awk命令
    • xargs
    • sort 排序命令
    • tr 替换命令
    • 考虑到服务器存在可能有无下载节点，即是否有网络节点，如果需要网络则要跳转至下载节点
  • 投递计算任务
  • 查看文件大小
  • • du命令查看看要处理恶的文件的大小
  • 下载任务---scp或是使用xftp其他软件
• 微生物宏基因组分析
• • ==profile==是什么?
  • 微生物宏基因组分析数据的获取
  • **实际操作**
  • • 构建snakemake流程进行生物信息分析
  • 构建流程----非snakemake 的并运行，模仿snakemake的运行模式
  • 通常来说会使用多种方法对数据进行处理，得到不同的结果，通过对比几个方案的不同数据，来获取最佳的数据进行后续处理同时也是一个证明数据，为你自己所选择的方法进行作证。
• 总结

ssh cngb-9 #cngb-9为一个计算节点，切换之后用户名@后面的部分会发生改变
#如果不知道节点怎么办，可以使用qstat来掉看节点状态
qstat -u \*  | tail -n +3 | awk -F'[ @]+' '$5=="r" && $8=="st.q" {print $9}' | awk -F'.' '{print $1}' | sort -V | uniq | tr '\n' ' ' | xargs -I xxx echo qhost -h xxx | xargs -I xxx bash -c xxx
#上面的qstat为查看节点状态，后面通过使用|通道进行优化。

awk -F'[ @]+' '$5=="r" && $8=="st.q" {print $9}'
#$n 中的n为提取第几列， -F是分隔符号的一个参数后面接分割符号，这里是@和 ' ',这个代码意思是将前面的数据以’ ‘和@分割成不同列，然后匹配出第五列等于'r'和第8列等于'st,q'的行的第九列输出出来。

 -V, --version-sort            在文本内进行自然版本排序

   将数据中的符号替换成你想要的符号

ssh software-install   # 只是切换节点而已每个可能名字不一样

qsub -clear -cwd -l vf=4g,num_proc=4 -P P_项目编号 -binding linear:4  -q st.q work.sh

```du -sh# 查看当前目录的大小du -sh #*查看当前目录下文件大小```

cp   root@192.168.0.101:~/filenotdir  ~   #从远端传送filenotdir文件到本地~ scp   root@192.168.0.101:/libopen*   /usr  #从远端传送以libopen开头的多个文件到本地 /usr scp   -r root@192.168.0.101:/ /usr/   #从远端传送文件夹到本地/usr ，注意-r 在本地命令帮助里没有！

                                WDNM,NMSL,CNM,CCC,NTMGLZGUN

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# 进行第一步质滤
mkdir -p 1.assay/fastp/ 1.assay/fastp/json/ 1.assay/fastp/html/ 1.assay/logs/fastp/ 2.runid/
cat sample.txt|while read line;doecho $line>lineinput_1=$(awk '{print$2}' line) input_2=$(awk '{print$3}' line) id=$(awk '{print$1}' line) export id=$idexport input_1=$input_1export input_2=$input_2echo /ldfssz1/ST_META/share/User/zhujie/.conda/envs/bioenv/bin/fastp -i $input_1 -I $input_2 -o 1.assay/fastp/$id.trimmed.1.fq.gz -O 1.assay/fastp/$id.trimmed.2.fq.gz -w 8 --length_required 30 --disable_adapter_trimming -j 1.assay/fastp/json/$id.json -h 1.assay/fastp/html/$id.html 2\>1.assay/logs/fastp/$id.fastp.log >fastp.shqsub -clear -cwd -l vf=8g,num_proc=4 -P P18Z10200N0127 -binding linear:4  -q st.q -o o.txt -e e.txt fastp.sh # sh  fastp.sh $id $input_1 $input_2#qsub -clear -cwd -l vf=4g,num_proc=4 -P P18Z10200N0127 -binding linear:4  -q st.q dofastp.sh#bowtie2去除人类的基因，进行比对，将人类的基因去除，由于我们要分析的数据为细菌基因，而人类基因常常占大多数所以去除改部分基因可以提高细菌中物种显著水平
bowtie2_index="/ldfssz1/ST_META/P18Z10200N0127_VC/tianliu/todo/03.stlfr/metastlfr/database/hg38/hg38"
#由于任务集群上运行的而该步骤要等前一步骤的样本完成才能进行所以要增加一个守门关#中间增加一个控制程序检测上一个程序运行了没有运行了就可以进行下一步操作
make -p 1.assay/logs/bowtie2/ 2.runid/ 1.assay/bowtie2/
cut -f 1 sample.txt|while read id;
doecho   /ldfssz1/ST_META/share/User/zhujie/.conda/envs/bioenv/bin/bowtie2 --very-sensitive -p 8 -x $bowtie2_index -1 1.assay/fastp/$id.trimmed.1.fq.gz -2 1.assay/fastq/$id.trimmed.2.fq.gz 2\> 1.assay/logs/bowtie2/$id.bowtie2_log \| samtools fastq -N -c 5 -f 12 -F 256 -1 1.assay/bowtie2/$id.rmhost.1.fq.gz -2 1.assay/bowtie2/$id.rmhost.2.fq.gz >sam.shqsub -clear -cwd -l vf=4g,num_proc=4 -P P18Z10200N0127 -binding linear:4  -q st.q -o o.txt -e e.txt sam.sh |awk '{print $3}' 1>>2.runid/sam.qsub.iddone