どうしてもPBHoneyをmacOS Sierraで動かしたい時
ゴール: macOS SierraでPBHoneyを動かす。
Softwares
Environment
Install Blasr
blasr 1.3.1をインストールする。ただし、Blasr 1.3.1はclangでビルドできない。
macOSのgccはclangなので、まずGCC 5を入れる。 5を入れたのは上のリンクで成功したと言っている人がいたから。
brew install gcc@5
次に、HDF5 1.8.14 をビルドして、brewのCellerに突っ込んでlinkしておく。
wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8.14/src/hdf5-1.8.14.tar.gz tar -xvvzf hdf5-1.8.14.tar.gz cd hdf5-1.8.14 mkdir -p /usr/local/Cellar/hdf5/1.8.14 CC=gcc-5 CXX=g++-5 ./configure --prefix /usr/local/Cellar/hdf5/1.8.14 --enable-cxx make make install brew link hdf5 # hdf5をインストールして**いない**場合 brew switch hdf5 1.8.14 # hdf5をインストールして**いる**場合
Blasrをインストールする
mkdir -p /usr/local/Cellar/blasr/2.2 cd blasr-smrtanalysis-2.2/ make HDF5INCLUDEDIR=/usr/local/opt/hdf5/include \ HDF5LIBDIR=/usr/local/opt/hdf5/lib \ CC=gcc-5 CXX=g++-5 # Homebrewはblasrのバージョンをurlから推測するので、 # Homebrew的には2.2 make install PREFIX=/usr/local/Cellar/blasr/2.2 brew link blasr
確認
blasr -version
以下の通り表示されれば成功
blasr 1.3.1
Install Samtools
samtools (0.1.17)をインストールする。
mkdir -p /usr/local/Cellar/samtools/0.1.17/bin/ wget -Osamtools-0.1.17.tar.gz https://github.com/samtools/samtools/archive/0.1.17.tar.gz tar -xvvzf samtools-0.1.17.tar.gz cd samtools-0.1.17 make CC=gcc-5 cp samtools /usr/local/Cellar/samtools/0.1.17/bin/ brew link samtools
Install pysam, numpy, h5py
pip install pysam numpy h5py
Install PBSuite
HOMEBREW_CC=gcc-5 HOMEBREW_CXX=g++-5 brew install pbsuite
~/.bash_profile
(もしくは使ってるシェルの設定)にPYTHONPATHを書いておく
export PYTHONPATH=/usr/local/opt/pbsuite:$PYTHONPATH
反映する
source ~/.bash_profile
Run Workflow
HoneyReadme.txt
を読む。
pyenv
のようなものを使っている人は2.7系にスイッチしておくこと。
pyenv shell 2.7.13
試しにワークフローを走らせる。
cd /usr/local/Cellar/pbsuite/14.7.14/docs/honeyExample ./workflow.sh
特にエラーがでなければOK. 以下の通り。
Mapping [INFO] 2017-03-11T15:06:44 [blasr] started. [INFO] 2017-03-11T15:07:21 [blasr] ended. Extracting Tails 2017-03-11 15:07:21,634 [INFO] Running /usr/local/bin/Honey.py pie mapping.sam lambda_modified.fasta 2017-03-11 15:07:21,634 [INFO] Extracting tails 2017-03-11 15:07:21,904 [INFO] Parsed 413 reads 2017-03-11 15:07:21,905 [INFO] Found 250 tails 2017-03-11 15:07:21,905 [INFO] 13 reads had double tails 2017-03-11 15:07:21,905 [INFO] Mapping Tails 2017-03-11 15:07:29,754 [INFO] [0, '[INFO] 2017-03-11T15:07:21 [blasr] started.\n[INFO] 2017-03-11T15:07:29 [blasr] ended.\n', None] 2017-03-11 15:07:29,754 [INFO] Consolidating alignments 2017-03-11 15:07:29,796 [INFO] 170 tails mapped Sam To Bam [samopen] SAM header is present: 1 sequences. Calling MD Tag [fai_load] build FASTA index. Calling Tails 2017-03-11 15:07:31,010 [INFO] Running /usr/local/bin/Honey.py tails mappingFinal.bam 2017-03-11 15:07:31,012 [INFO] Parsing Reads 2017-03-11 15:07:31,039 [INFO] Writing Results 2017-03-11 15:07:31,039 [INFO] Chrom lambda_NEB3011_lambda_NEB3011 made 113 pre-filter clusters 2017-03-11 15:07:31,041 [INFO] Chrom lambda_NEB3011_lambda_NEB3011 made 5 post-filter clusters 2017-03-11 15:07:31,041 [INFO] Finished Calling Spots 2017-03-11 15:07:31,662 [INFO] Running /usr/local/bin/Honey.py spots mappingFinal.bam 2017-03-11 15:07:31,678 [INFO] making container for lambda_NEB3011 (lambda_NEB3011:0-48802 48802 bp) 2017-03-11 15:07:31,681 [INFO] parsing bam 2017-03-11 15:07:31,699 [INFO] 583 reads to parse 2017-03-11 15:07:31,746 [INFO] parsed 18 reads (3 % complete) 2017-03-11 15:07:31,766 [INFO] parsed 24 reads (4 % complete) 2017-03-11 15:07:31,786 [INFO] parsed 30 reads (5 % complete) ... 2017-03-11 15:07:32,970 [INFO] parsed 572 reads (98 % complete) 2017-03-11 15:07:32,976 [INFO] parsed 578 reads (99 % complete) 2017-03-11 15:07:32,982 [INFO] parsed 583 reads (100 % complete) 2017-03-11 15:07:32,982 [INFO] parsed 583 reads 2017-03-11 15:07:32,998 [INFO] calling spots 2017-03-11 15:07:33,034 [INFO] MaxCov:32 MeanCov:16 StdCov:5 MinCov:0 2017-03-11 15:07:33,034 [INFO] MIS processing 2017-03-11 15:07:33,046 [INFO] RateMean 0.042394 -- RateStd 0.010260 2017-03-11 15:07:33,049 [INFO] MaxSig: 0.040435 MeanSig: 0.000013 StdSig 0.005060 MinSig: -0.052323 2017-03-11 15:07:33,049 [INFO] 0 MIS entries 2017-03-11 15:07:33,050 [INFO] INS processing 2017-03-11 15:07:33,063 [INFO] RateMean 0.000718 -- RateStd 0.002610 2017-03-11 15:07:33,067 [INFO] MaxSig: 0.045733 MeanSig: 0.000000 StdSig 0.002097 MinSig: -0.046218 2017-03-11 15:07:33,069 [INFO] 1 INS entries 2017-03-11 15:07:33,070 [INFO] DEL processing 2017-03-11 15:07:33,081 [INFO] RateMean 0.044015 -- RateStd 0.052830 2017-03-11 15:07:33,082 [INFO] MaxSig: 0.396365 MeanSig: 0.000004 StdSig 0.024411 MinSig: -0.428616 2017-03-11 15:07:33,083 [INFO] 1 DEL entries 2017-03-11 15:07:33,083 [INFO] Filtering INS results 2017-03-11 15:07:33,121 [INFO] found 1 spots 2017-03-11 15:07:33,131 [INFO] finished 583 reads 2017-03-11 15:07:33,132 [INFO] finished 1 spots