[TOC]
安装Boost C++ library
安装pIRS过程中遇到未安装Boost C++ library的问题
从这里下载 https://www.boost.org/
下载boost_1_68_0版本
tar xzvf boost_1_68_0.tgz.gz
$ cd path/to/boost_1_67_0
$ ./bootstrap.sh --prefix=path/to/installation/prefix
$ sudo ./b2 install
./bootstrap.sh这步我自己添加了 --with-python=python3 --with-python-version=3.6这两个参数，因为我单独运行./bootstrap.sh的时候发现它自动检测到的是ubuntu18.10自带的python2，我希望它与python3关联。
./b2这步需要加sudo 不加的话会有些文件安装不上permission denied。
安装步骤可以参考这两个
https://www.boost.org/doc/libs/1_68_0/more/getting_started/unix-variants.html
https://blog.csdn.net/lvyibin890/article/details/80888554
安装pIRS
从这里下载pIRS压缩包 https://github.com/galaxy001/pirs
cd path/to/pIRS
make
sudo -s
find . -type l|while read a;do cp --copy-contents -LR "$a" /TARGET/PATH/;done
试用pIRS
安装后在任意目录输入pirs即可调用pIRS程序
Program: pirs (Profile-based Illumina pair-end Reads Simulator)
Version: 2.0.0
Author: Jianying Yuan (BGI-Shenzhen)
Contact: [email protected]
Compile Date: Nov 17 2018 time: 21:31:02
Usage: pirs [option]
diploid generate diploid genome.
simulate simulate Illumina reads.
但是运行命令的时候遇到错误：
pirs simulate sample.fa
[pIRS] Program: pirs (Profile-based Illumina pair-end Reads Simulator)
[pIRS] Version: 2.0.0
[pIRS] Author: Jianying Yuan (BGI-Shenzhen)
[pIRS] Contact: [email protected]
[pIRS] Compile Date: Nov 17 2018 time: 21:30:49
[pIRS] Current time: Sun Nov 18 16:02:45 2018
[pIRS] Command line: pirs simulate sample.fa
[pIRS]
[pIRS] Loading base-calling profile /usr/local/share/pirs/Base-Calling_Profiles/humNew.PE100.matrix.gz
************************************************************
[pIRS] FATAL ERROR:
Failed to open the file "/usr/local/share/pirs/Base-Calling_Profiles/humNew.PE100.matrix.gz": No such file or directory
************************************************************
发现pIRS的安装目录下有两组Profiles,将其中一组移动到
sudo mv Base-Calling_Profiles -t /usr/local/share/pirs/
sudo mv GC-depth_Profiles -t /usr/local/share/pirs/
sudo mv InDel_Profiles -t /usr/local/share/pirs/
然后运行
pirs simulate sample.fa
[pIRS] Program: pirs (Profile-based Illumina pair-end Reads Simulator)
[pIRS] Version: 2.0.0
[pIRS] Author: Jianying Yuan (BGI-Shenzhen)
[pIRS] Contact: [email protected]
[pIRS] Compile Date: Nov 17 2018 time: 21:30:49
[pIRS] Current time: Sun Nov 18 16:08:32 2018
[pIRS] Command line: pirs simulate sample.fa
[pIRS]
[pIRS] Loading base-calling profile /usr/local/share/pirs/Base-Calling_Profiles/humNew.PE100.matrix.gz
[pIRS] Loaded base-calling profile header:
[pIRS] num_ref_bases = 4
[pIRS] num_cycles = 200
[pIRS] num_seq_bases = 4
[pIRS] num_quality_scores = 41
[pIRS] Loading DistMatrix of base-calling profile
[pIRS] Loading QTransMatrix of base-calling profile
[pIRS] Done loading Base-Calling profile.
[pIRS] Loading InDel error profile /usr/local/share/pirs/InDel_Profiles/phixv2.InDel.matrix
[pIRS] Indel error profile statistics:
[pIRS] max_indel_len = 3
[pIRS] num_cycles = 200
[pIRS] read_1_count = 147091454
[pIRS] read_2_count = 145785569
[pIRS] Insertion-bp rate of 100-bp read 1 = 0.000478%
[pIRS] Deletion-bp rate of 100-bp read 1 = 0.001118%
[pIRS] Insertion-bp rate of 100-bp read 2 = 0.000837%
[pIRS] Deletion-bp rate of 100-bp read 2 = 0.001551%
[pIRS] Done loading InDel error profile.
[pIRS] Loading GC bias profile /usr/local/share/pirs/GC-depth_Profiles/humNew.gcdep_200.dat
[pIRS] GC bias profile (GC content, relative abundance), showing every 10%
[pIRS] 0% 0.00422544
[pIRS] 10% 0.0909624
[pIRS] 20% 0.782551
[pIRS] 30% 0.966385
[pIRS] 40% 0.950876
[pIRS] 50% 0.783616
[pIRS] 60% 0.554585
[pIRS] 70% 0.260476
[pIRS] 80% 0.0578053
[pIRS] 90% 0.00422544
[pIRS] 100% 0.00422544
[pIRS] Done loading GC bias profile.
[pIRS]
[pIRS] Beginning simulation with the following parameters:
[pIRS]
[pIRS] Read length: 100
[pIRS] Insert length mean: 180
[pIRS] Insert length standard deviation: 18
[pIRS] Coverage: 5
[pIRS] Diploid: no
[pIRS] Cyclized (jumping library): no
[pIRS] Simulate substitution errors: yes
[pIRS] Substitution error rate: default of base-calling profile
[pIRS] Base-calling profile: /usr/local/share/pirs/Base-Calling_Profiles/humNew.PE100.matrix.gz
[pIRS] Substitution error algorithm: quality transition mode algorithm
[pIRS] Simulate InDel errors: yes
[pIRS] InDel error profile: /usr/local/share/pirs/InDel_Profiles/phixv2.InDel.matrix
[pIRS] Simulate GC content bias: yes
[pIRS] GC bias profile: /usr/local/share/pirs/GC-depth_Profiles/humNew.gcdep_200.dat
[pIRS] Output type: text
[pIRS] Output directory: .
[pIRS] Indiv name:
[pIRS] Simulate quality values: yes
[pIRS] ASCII shift of quality value 33
[pIRS] Mode of mask quality: None
[pIRS] Random seed: 7510571324928
[pIRS] Number of simulator threads: 2
[pIRS]
[pIRS] Reading scaffold "DH10BmutV2_3046486_0_0_0_0_0_926968" into memory
[pIRS] Simulating reads from scaffold "DH10BmutV2_3046486_0_0_0_0_0_926968" (length = 226)
[pIRS] Simulated 5 of 5 read pairs
[pIRS] Done simulating reads from scaffold "DH10BmutV2_3046486_0_0_0_0_0_926968" (length = 226)
[pIRS] Reading scaffold "DH10BmutV2_1779373_1_0_2_0_0_761290" into memory
[pIRS] Simulating reads from scaffold "DH10BmutV2_1779373_1_0_2_0_0_761290" (length = 205)
[pIRS] Simulated 5 of 5 read pairs
[pIRS] Done simulating reads from scaffold "DH10BmutV2_1779373_1_0_2_0_0_761290" (length = 205)
[pIRS] Reading scaffold "DH10BmutV2_106571_1_0_0_0_0_933953" into memory
[pIRS] Simulating reads from scaffold "DH10BmutV2_106571_1_0_0_0_0_933953" (length = 172)
[pIRS] Simulated 4 of 4 read pairs
[pIRS] Done simulating reads from scaffold "DH10BmutV2_106571_1_0_0_0_0_933953" (length = 172)
[pIRS] Reading scaffold "DH10BmutV2_1890995_0_0_1_0_1_838382" into memory
[pIRS] Simulating reads from scaffold "DH10BmutV2_1890995_0_0_1_0_1_838382" (length = 212)
[pIRS] Simulated 5 of 5 read pairs
[pIRS] Done simulating reads from scaffold "DH10BmutV2_1890995_0_0_1_0_1_838382" (length = 212)
[pIRS] Reading scaffold "DH10BmutV2_1695593_0_0_2_5_0_261534" into memory
[pIRS] Simulating reads from scaffold "DH10BmutV2_1695593_0_0_2_5_0_261534" (length = 189)
[pIRS] Simulated 4 of 4 read pairs
[pIRS] Done simulating reads from scaffold "DH10BmutV2_1695593_0_0_2_5_0_261534" (length = 189)
[pIRS] Reading scaffold "DH10BmutV2_869560_1_0_1_0_1_154195" into memory
[pIRS] Simulating reads from scaffold "DH10BmutV2_869560_1_0_1_0_1_154195" (length = 192)
[pIRS] Simulated 4 of 4 read pairs
[pIRS] Done simulating reads from scaffold "DH10BmutV2_869560_1_0_1_0_1_154195" (length = 192)
[pIRS] Reading scaffold "DH10BmutV2_4659073_0_0_2_1_1_219617" into memory
[pIRS] Simulating reads from scaffold "DH10BmutV2_4659073_0_0_2_1_1_219617" (length = 215)
Floating point exception (core dumped)
运行产生的文件如下图
pirs运行结果.png
pirs运行结果2.png
遇到Floating point exception (core dumped)错误
This error comes when there is some expression dividing value by zero. eg. x=10 and y=0 and x/y. This means, x is divided by zero, which results to floating point error.
But 代码并不是我写的而且代码应该不会有错吧。。。
ubuntu系统报错：ubuntu nautilus[3832]:can`t init metadata tree /home/sjl/.local/share/gvfs-metadata/root:open:Permission denied
暂缓此问题。
https://stackoverflow.com/questions/17299894/floating-point-exception-core-dumped
https://www.linuxquestions.org/questions/linux-newbie-8/floating-point-exception-core-dumped-899988/
http://blog.51cto.com/liuqunying/1624423
参考
https://github.com/galaxy001/pirs
这个文章里还有其他软件的对比
https://www.zd200572.com/2017/10/14/WES-executing-process/