SMURF-Science封面文章使用的16S新流程

# 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 MCR
wget 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/glnxa64
export 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.git
cd 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.gz

% ********************** 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.m

chmod +x ./StandaloneVersion/SMURF_lin
 time ./StandaloneVersion/SMURF_lin ./Configs/compiled_params_script.m

```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 0m38.527s