# 下载依赖的matlab MCR平台（作者使用matlab写的分析软件）虽然这是美帝的，但是学习先进技术嘛！mkdir MCR && cd MCRwget https://www.mathworks.com/supportfiles/downloads/R2014a/deployment_files/R2014a/installers/glnxa64/MCR_R2014a_glnxa64_installer.zip unzip MCR_R2014a_glnxa64_installer.zip# 安装下，必须有图形界面才能安装成功。sudo ./install# 设置环境变量，这里是临时的，所以退出终端后埼再添加一次export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/MATLAB/MATLAB_Compiler_Runtime/v83/runtime/glnxa64:/usr/local/MATLAB/MATLAB_Compiler_Runtime/v83/bin/glnxa64:/usr/local/MATLAB/MATLAB_Compiler_Runtime/v83/sys/os/glnxa64export XAPPLRESDIR=/usr/local/MATLAB/MATLAB_Compiler_Runtime/v83/X11/app-defaults# 报了个这个，因为找不到图形界面，算法不需要，应该不影响#Exception in thread "main" java.lang.InternalError: Can't connect to X11 window server using ':0' as the value of the DISPLAY variable.cd ..# 下载脚本# https://github.com/NoamShental/SMURF.git# 我把它拉到了gitee上，克隆速度快上许多，特别是这个，因为挺大的git clone https://github.com/NoamShental/SMURF.gitcd SMURF# 数据库准备cat ./Green_Genes_201305/unique_up_to_3_ambiguous_16S/GreenGenes_201305_unique_up_to_3_ambiguous_16S.fasta.gz*> ./Green_Genes_201305/unique_up_to_3_ambiguous_16S/Green_Genes_201305_unique_up_to_3_ambiguous_16S.fasta.gz gunzip ./Green_Genes_201305/unique_up_to_3_ambiguous_16S/Green_Genes_201305_unique_up_to_3_ambiguous_16S.fasta.gz123456789101112131415161718192021
运行与结果
运行好像一条命令就行了，前提是配置好引物等参数。 需要修改的参数：
% ********************** GENERAL PARAMETERS ******************** base_samples_dir = '/'; ... % ********************** SAMPLE PREP PARAMETERS ******************** % Set the 16S reference DB uniS16_dir = './Green_Genes_201305/unique_up_to_3_ambiguous_16S'; db_filename = 'Green_Genes_201305_unique_up_to_3_ambiguous_16S'; # 其他参数，不确定是否需要 vi Configs/db_params_script.m #把 ../ 替换为./或者在Standalone文件夹运行，不需要改 vi Configs/adhoc_db_params_script.m1234567891011
运行啦
chmod +x ./StandaloneVersion/SMURF_lin time ./StandaloneVersion/SMURF_lin ./Configs/compiled_params_script.m12
当然，示例文件肯定不会报错，很轻松出结果嘛。
```bash time ./StandaloneVersion/SMURF_lin ./Configs/compiled_params_script.m Doing quality filters Part 1/1 - Block 1/5 Part 1/1 - Block 2/5 Part 1/1 - Block 3/5 Part 1/1 - Block 4/5 Part 1/1 - Block 5/5 Number of reads: 472350 Percent of long enough reads: 0.94713 Percent of good reads: 0.91592 Counting fasta write: 1 Elapsed time is 9.831863 seconds. Mapped to primers 82% of unique reads Mapped to primers 97% of read counts regions_files = 6x1 struct array with fields: name date bytes isdir datenum ans = ./Green_Genes_201305/unique_up_to_3_ambiguous_16S_amp6Regions_2mm_RL130/GreenGenes_201305_unique_up_to_3_ambiguous_16S_amp6Regions_2mm_RL130_region1.mat Loading bacterial DB for region 1 out of 6 from original region 1 Loading bacterial DB for region 2 out of 6 from original region 2 Loading bacterial DB for region 3 out of 6 from original region 3 Loading bacterial DB for region 4 out of 6 from original region 4 Loading bacterial DB for region 5 out of 6 from original region 5 Loading bacterial DB for region 6 out of 6 from original region 6 Region 1 out of 6 Keep high freq: 28% of reads Keep high freq: 91% of counts Building matrix M Building matrix Q -------------------------------------------- ... -------------------------------------------- Region 6 out of 6 Keep high freq: 2% of reads Keep high freq: 89% of counts Building matrix M Building matrix Q -------------------------------------------- Region 1 out of 6 Keeping reads matched to DB: 95% of reads Keeping reads matched to DB: 98% of counts -------------------------------------------- ... -------------------------------------------- Region 6 out of 6 Keeping reads matched to DB: 97% of reads Keeping reads matched to DB: 100% of counts -------------------------------------------- Filter out columns (bacteria) Normalize frequency counts Build matrix A_L2 Iter:4674. Error reduction of X (L1 norm): 9.7149e-07 Total iterations time: 60.4761 Error using main_multiple_regions (line 34) Not enough input arguments. Error in main_smurf (line 36)
MATLAB:minrhs
real 9m1.616s user 11m32.462s sys 0m38.527s12345678910111213141516171819202122232425262728293031323334353637383940414243444546474849505152535455565758596061626364656667686970
