RaptorX-3DModeling をテンプレートにして作成
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開始行:
本家様[[http://raptorx.uchicago.edu/>+http://raptorx.uchi...
参照先[[https://qiita.com/Ag_smith/items/9e6a29faa719be64...
***下準備 [#a5013d2f]
#code(nonumber){{
yum install epel-release
yum install cmake python3 openmpi-devel dssp screen wget ...
mkdir -p /apps/src
}}
#code(nonumber){{
yum localinstall cuda-repo-rhel7-11-2-local-11.2.0_460.27...
yum install cuda-11-2
yum localinstall cuda-repo-rhel7-10-2-local-10.2.89-440.3...
yum install yum install cuda-libraries-dev-10-2
yum remove "cuda-repo*"
}}
#code(nonumber){{
tar zxvf cudnn-10.2-linux-x64-v7.6.5.32.tgz
cp -rp cuda/include/cudnn.h /usr/local/cuda-10.2/include/
cp -rp cuda/lib64/* /usr/local/cuda-10.2/lib64/
cp -rp cuda/NVIDIA_SLA_cuDNN_Support.txt /usr/local/cuda-...
}}
&size(10){「site-packages/theano/gpuarray/dnn.py」から「c...
&size(10){カードの問題なのか不明だが、10.2ではGPUで計算出...
***pdbx [#c59b86c9]
#code(nonumber){{
[root@centos7 ~]# cd /apps/
[root@centos7 apps]# git clone https://github.com/soeding...
[root@centos7 apps]# cd pdbx/
[root@centos7 pdbx]# mkdir build && cd $_
[root@centos7 build]# cmake ..
[root@centos7 build]# make && make install
}}
pythonライブラリが「/usr/local/lib/python3.6/site-package...
***legacy blast [#wfe8c9f4]
legacy blastの最新版 2.2.26
#code(nonumber){{
[root@centos7 ~]# cd /apps/src
[root@centos7 src]# curl -O ftp://ftp.ncbi.nlm.nih.gov/bl...
[root@centos7 src]# cd ..
[root@centos7 apps]# tar xzf src/blast-2.2.26-x64-linux.t...
}}
***psipred [#mdeea381]
#code(nonumber){{
[root@centos7 ~]# cd /apps/
[root@centos7 apps]# git clone https://github.com/psipred...
[root@centos7 apps]# cd psipred
[root@centos7 psipred]# git checkout -b 4.0 refs/tags/v4.0
Switched to a new branch '4.0'
[root@centos7 psipred]# cd src
[root@centos7 src]# make && make install
[root@centos7 src]# cd /apps/psipred/
[root@centos7 psipred]#
[root@centos7 psipred]# ls -CF
bin/ BLAST+/ data/ example/ LICENSE README runpsipr...
[root@centos7 psipred]#
[root@centos7 psipred]# ls -l bin/
total 68
-rwxr-xr-x. 1 root root 13736 Jan 29 01:45 chkparse
-rwxr-xr-x. 1 root root 18240 Jan 29 01:45 psipass2
-rwxr-xr-x. 1 root root 13744 Jan 29 01:45 psipred
-rwxr-xr-x. 1 root root 13464 Jan 29 01:45 seq2mtx
[root@centos7 psipred]#
}}
***HHSuite [#o802b776]
#code(nonumber){{
[root@centos7 ~]# cd /apps/src
[root@centos7 src]# git clone https://github.com/soeding...
[root@centos7 src]# cd hh-suite/
[root@centos7 hh-suite]# git checkout -b 3.3.0 refs/tags/...
Switched to a new branch '3.3.0'
[root@centos7 hh-suite]#
[root@centos7 hh-suite]# mkdir build && cd $_
[root@centos7 build]# module load mpi/openmpi-x86_64
[root@centos7 build]# cmake -DCMAKE_INSTALL_PREFIX=/apps/...
[root@centos7 build]# make && make install
[root@centos7 build]# ls -l /apps/hh-suite/3.3/
total 8
drwxr-xr-x. 2 root root 4096 Jan 29 01:33 bin
drwxr-xr-x. 2 root root 167 Jan 29 01:33 data
drwxr-xr-x. 2 root root 4096 Jan 29 01:33 scripts
[root@centos7 build]#
}}
設定
#code(nonumber){{
[root@centos7 ~]# vi /apps/hh-suite/3.3/scripts/HHPaths.pm
}}
#code(diff,nonumber){{
--- /apps/hh-suite/3.3/scripts/HHPaths.pm.orig 2021-02-0...
+++ /apps/hh-suite/3.3/scripts/HHPaths.pm 2021-02-0...
@@ -38,18 +38,18 @@
#our $execdir = ".../psipred/bin"; # path to PSI...
#our $datadir = ".../psipred/data"; # path to PSI...
#our $ncbidir = ".../blast/bin"; # path to NCB...
-our $execdir = "/cluster/toolkit/production/bioprogs/psi...
-our $datadir = "/cluster/toolkit/production/bioprogs/psi...
-our $ncbidir = "/cluster/toolkit/production/bioprogs/bla...
+our $execdir = "/apps/psipred/bin"; # path to PSIPRED V...
+our $datadir = "/apps/psipred/data"; # path to PSIPRED V...
+our $ncbidir = "/apps/blast-2.2.26/bin"; # path to NC...
########################################################...
# PLEASE COMPLETE THE PATHS ... TO YOUR LOCAL PDB FILES,...
#our $pdbdir = ".../pdb/all"; # where are t...
#our $dsspdir = ".../dssp/data"; # where are t...
#our $dssp = ".../dssp/bin/dsspcmbi"; # where is th...
-our $pdbdir = "/cluster/databases/pdb/all"; ...
-our $dsspdir = "/cluster/databases/dssp/data"; ...
-our $dssp = "/cluster/databases/dssp/bin/dsspcmbi"; ...
+our $pdbdir = "/Public/databases/pdb/divided"; ...
+our $dsspdir = "/Public/databases/dssp/data"; ...
+our $dssp = "/usr/bin/mkdssp"; # where is the dssp ...
########################################################...
# The lines below probably do not need to be changed
}}
***PDBファイル/DSSPデータベース/HH-suiteデータファイルの...
保存場所の確保
#code(nonumber){{
[root@centos7 ~]# mkdir /Public
[root@centos7 ~]# mount -t nfs qnap:/Public /Public
[root@centos7 ~]# mkdir -p /Public/databases/pdb/divided ...
}}
-PDBファイルの取得
#code(nonumber){{
[root@centos7 ~]# cd /Public/databases/pdb/divided
[root@centos7 divided]# rsync -avz --delete ftp.pdbj.org:...
[root@centos7 divided]# du -hs .
34G .
[root@centos7 divided]# find . -name *.ent.gz -exec /usr/...
}}
解凍前が34GBで解凍すると176GB. 解凍前のファイルはそのまま...
-DSSPデータベースの取得
「rsync://rsync.cmbi.umcn.nl/dssp-from-mmcif/」を参照元に...
#code(nonumber){{
[root@centos7 ~]# rsync -avz --delete rsync://rsync.cmbi....
[root@centos7 ~]# du -hs /Public/databases/dssp/
29G /Public/databases/dssp/
[root@centos7 ~]#
[root@centos7 ~]# ls -l /Public/databases/dssp/data | wc -l
169765
[root@centos7 ~]#
[root@centos7 ~]# find /Public/databases/dssp/data -name ...
169764
[root@centos7 ~]#
}}
だいたい29GBになります. こちらは平文. 総数は 169,764枚
-HH-suite向けのデータファイルを取得
[[http://wwwuser.gwdg.de/~compbiol/uniclust/>+http://wwwu...
#code(nonumber){{
[root@centos7 ~]# cd /Public/databases/HH-suite
[root@centos7 HH-suite]# wget http://wwwuser.gwdg.de/~com...
[root@centos7 HH-suite]# tar xzf UniRef30_2020_06_hhsuite...
[root@centos7 HH-suite]# ls -lh
total 228G
-rw-------. 1 528745 47148 140G Oct 5 21:17 UniRef30_202...
-rw-------. 1 528745 47148 671M Oct 5 21:17 UniRef30_202...
-rw-------. 1 528745 47148 6.0G Oct 5 21:13 UniRef30_202...
-rw-------. 1 528745 47148 605M Oct 5 21:14 UniRef30_202...
-rw-------. 1 528745 47148 35G Oct 5 21:18 UniRef30_202...
-rw-------. 1 528745 47148 20M Oct 5 21:18 UniRef30_202...
-rw-r--r--. 1 root root 47G Feb 1 05:20 UniRef30_202...
-rw-------. 1 528745 47148 379 Oct 7 02:26 UniRef30_202...
[root@centos7 HH-suite]# chmod 644 ./*
[root@centos7 HH-suite]# du -hs .
228G .
[root@centos7 HH-suite]#
}}
176GB＋29GB＋228GB = 433GB
***pyenv/anaconda環境 [#zf8e21f9]
#code(nonumber){{
[root@centos7 ~]# git clone https://github.com/yyuu/pyenv...
[root@centos7 ~]# export PYENV_ROOT=/apps/pyenv
[root@centos7 ~]# export PATH=$PYENV_ROOT/bin:$PATH
[root@centos7 ~]# eval "$(pyenv init - --no-rehash)"
[root@centos7 ~]# pyenv install anaconda3-5.3.1
[root@centos7 ~]# pyenv global anaconda3-5.3.1
[root@centos7 ~]# export PATH=$PYENV_ROOT/versions/anacon...
[root@centos7 ~]# conda update conda
[root@centos7 ~]# conda create -n RaptorX python=2
[root@centos7 ~]# source activate RaptorX
(RaptorX) [root@centos7 ~]# which python2.7
/apps/pyenv/versions/anaconda3-5.3.1/envs/RaptorX/bin/pyt...
(RaptorX) [root@centos7 ~]# conda install numpy nose
(RaptorX) [root@centos7 ~]# conda install -c anaconda msg...
(RaptorX) [root@centos7 ~]# pip install biopython==1.76
(RaptorX) [root@centos7 ~]# conda install pillow
(RaptorX) [root@centos7 ~]# conda install numpy scipy mkl
(RaptorX) [root@centos7 ~]# conda install theano pygpu
(RaptorX) [root@centos7 ~]# mkdir -p /apps/src && cd $_
(RaptorX) [root@centos7 src]# git clone https://github.co...
(RaptorX) [root@centos7 src]# cd shared_ndarray/
(RaptorX) [root@centos7 shared_ndarray]# python2.7 setup....
(RaptorX) [root@centos7 ~]# cd /apps/src
(RaptorX) [root@centos7 src]# tar jxvf PyRosetta4.Release...
(RaptorX) [root@centos7 src]# mv PyRosetta4.Release.pytho...
(RaptorX) [root@centos7 src]# cd PyRosetta4_python27_274/...
(RaptorX) [root@centos7 setup]# python setup.py build
(RaptorX) [root@centos7 setup]# python setup.py install
(RaptorX) [root@centos7 ~]# cd /apps
(RaptorX) [root@centos7 apps]# git clone https://github.c...
(RaptorX) [root@centos7 apps]# cd RaptorX-3DModeling
(RaptorX) [root@centos7 RaptorX-3DModeling]# vi raptorx-e...
}}
#code(diff,nonumber){{
--- /apps/RaptorX-3DModeling/raptorx-external.sh.orig 2...
+++ /apps/RaptorX-3DModeling/raptorx-external.sh 2...
@@ -1,9 +1,9 @@
## the install folder of the hhsuite package, needed for...
-export HHDIR=/mnt/data/RaptorXCommon/HHblits/hhsuite-3.2...
+export HHDIR=/apps/hh-suite/3.3
export PATH=$HHDIR/bin:$HHDIR/scripts:$PATH
## the location of the HHM database to be searched by HH...
-export HHDB=/mnt/data/RaptorXCommon/HHblits/DB/uniref30_...
+export HHDB=/Public/databases/HH-suite/UniRef30_2020_06
## the location of the metagenome data file to be search...
export MetaDB=/mnt/data/conmod_databases/metaclust_serie...
}}
#code(nonumber){{
(RaptorX) [root@centos7 ~]# export ModelingHome=/apps/Rap...
}}
「http://raptorx.uchicago.edu/download/」にて登録を行い「...
#code(nonumber){{
(RaptorX) [root@centos7 ~]# cd $ModelingHome/DL4DistanceP...
(RaptorX) [root@centos7 DL4DistancePrediction4]# tar xf /...
(RaptorX) [root@centos7 DL4DistancePrediction4]# cd $Mode...
(RaptorX) [root@centos7 DL4PropertyPrediction]# tar xf /a...
}}
***HH-Suiteのテスト [#z2a4ba75]
#code(nonumber){{
[illya@centos7 ~]$ mkdir test && cd $_
[illya@centos7 test]$ cp /apps/src/hh-suite/data/query.se...
[illya@centos7 test]$ cat query.seq
>sp|Q5VUD6|FA69B_HUMAN Protein FAM69B OS=Homo sapiens GN=...
MRRLRRLAHLVLFCPFSKRLQGRLPGLRVRCIFLAWLGVFAGSWLVYVHYSSYSERC...
RDKDVTIKCGIEETLDSKARSDAAPRRELVLFDKPTRGTSIKEFREMTLSFLKANLG...
HASRLLGYCGDLYLTEGVPHGAWHAAALPPLLRPLLPPALQGALQQWLGPAWPWRAK...
VRRFLQGRRCEHSTDCTYGRDCRAPCDRLMRQCKGDLIQPNLAKVCALLRGYLLPGA...
[illya@centos7 test]$ /apps/hh-suite/3.3/bin/hhblits -cpu...
- 12:20:21.914 INFO: Search results will be written to qu...
- 12:20:21.914 INFO: Search results will be written to qu...
- 12:20:38.622 INFO: Searching 25985124 column state sequ...
- 12:20:38.675 INFO: query.seq is in A2M, A3M or FASTA fo...
- 12:20:38.675 INFO: Iteration 1
- 12:20:38.867 INFO: Prefiltering database
- 12:22:00.098 INFO: HMMs passed 1st prefilter (gapless p...
- 12:22:02.105 INFO: HMMs passed 2nd prefilter (gapped pr...
- 12:22:02.105 INFO: HMMs passed 2nd prefilter and not fo...
- 12:22:02.105 INFO: Scoring 419 HMMs using HMM-HMM Viter...
- 12:22:02.299 INFO: Alternative alignment: 0
- 12:22:23.947 INFO: 419 alignments done
- 12:22:23.948 INFO: Alternative alignment: 1
- 12:22:24.044 INFO: 415 alignments done
- 12:22:24.045 INFO: Alternative alignment: 2
- 12:22:24.075 INFO: 56 alignments done
- 12:22:24.075 INFO: Alternative alignment: 3
- 12:22:24.087 INFO: 4 alignments done
- 12:22:25.010 INFO: Premerge done
- 12:22:25.011 INFO: Realigning 318 HMM-HMM alignments us...
- 12:22:26.674 INFO: 94 sequences belonging to 94 databas...
- 12:22:26.674 INFO: Number of effective sequences of res...
Query sp|Q5VUD6|FA69B_HUMAN Protein FAM69B OS=Hom...
Match_columns 431
No_of_seqs 520 out of 780
Neff 6.52866
Searched_HMMs 419
Date Tue Feb 2 12:22:26 2021
Command /apps/hh-suite/3.3/bin/hhblits -cpu 4 -i qu...
No Hit Prob E-value P-value ...
1 UniRef100_A0A024R8I5 Family wi 100.0 2E-172 5E-178 ...
2 UniRef100_UPI000C879985 protei 100.0 4E-160 9E-166 ...
:
[illya@centos7 test]$
}}
***RaptorX-3DModeling [#u294b1b7]
テスト
参照元と同じく2O6Pで
#code(nonumber){{
[illya@centos7 ~]$ cd test
[illya@centos7 test]$ vi 2o6pA.fasta
>2O6P_1|Chains A,B|Iron-regulated surface determinant pro...
NAADSGTLNYEVYKYNTNDTSIANDYFNKPAKYIKKNGKLYVQITVNHSHWITGMSI...
TYKFNGPTDVAGAN
[illya@centos7 test]$
[illya@centos7 test]$ export PYENV_ROOT=/apps/pyenv
[illya@centos7 test]$ export PATH=$PYENV_ROOT/bin:$PATH
[illya@centos7 test]$ eval "$(pyenv init - --no-rehash)"
[illya@centos7 test]$ export PATH=$PYENV_ROOT/versions/an...
[illya@centos7 test]$ export CUDA_ROOT=/usr/local/cuda-10.2
[illya@centos7 test]$ source activate RaptorX
(RaptorX) [illya@centos7 test]$
(RaptorX) [illya@centos7 test]$ export ModelingHome=/apps...
(RaptorX) [illya@centos7 test]$ . $ModelingHome/raptorx-p...
(RaptorX) [illya@centos7 test]$ . $ModelingHome/raptorx-e...
(RaptorX) [illya@centos7 test]$ /apps/RaptorX-3DModeling/...
(略)/RaptorXFolder.sh [ -o outDir | -g gpu | -m MSAmethod...
This script predicts angle/contact/distance/orien...
ModelingHome=/apps/RaptorX-3DModeling
Please make sure that ModelingHome is cor...
Before running this script, some external...
inputFile: a protein primary sequence file in FAS...
:
:
(RaptorX) [illya@centos7 test]$ /apps/RaptorX-3DModeling/...
}}
終了行:
本家様[[http://raptorx.uchicago.edu/>+http://raptorx.uchi...
参照先[[https://qiita.com/Ag_smith/items/9e6a29faa719be64...
***下準備 [#a5013d2f]
#code(nonumber){{
yum install epel-release
yum install cmake python3 openmpi-devel dssp screen wget ...
mkdir -p /apps/src
}}
#code(nonumber){{
yum localinstall cuda-repo-rhel7-11-2-local-11.2.0_460.27...
yum install cuda-11-2
yum localinstall cuda-repo-rhel7-10-2-local-10.2.89-440.3...
yum install yum install cuda-libraries-dev-10-2
yum remove "cuda-repo*"
}}
#code(nonumber){{
tar zxvf cudnn-10.2-linux-x64-v7.6.5.32.tgz
cp -rp cuda/include/cudnn.h /usr/local/cuda-10.2/include/
cp -rp cuda/lib64/* /usr/local/cuda-10.2/lib64/
cp -rp cuda/NVIDIA_SLA_cuDNN_Support.txt /usr/local/cuda-...
}}
&size(10){「site-packages/theano/gpuarray/dnn.py」から「c...
&size(10){カードの問題なのか不明だが、10.2ではGPUで計算出...
***pdbx [#c59b86c9]
#code(nonumber){{
[root@centos7 ~]# cd /apps/
[root@centos7 apps]# git clone https://github.com/soeding...
[root@centos7 apps]# cd pdbx/
[root@centos7 pdbx]# mkdir build && cd $_
[root@centos7 build]# cmake ..
[root@centos7 build]# make && make install
}}
pythonライブラリが「/usr/local/lib/python3.6/site-package...
***legacy blast [#wfe8c9f4]
legacy blastの最新版 2.2.26
#code(nonumber){{
[root@centos7 ~]# cd /apps/src
[root@centos7 src]# curl -O ftp://ftp.ncbi.nlm.nih.gov/bl...
[root@centos7 src]# cd ..
[root@centos7 apps]# tar xzf src/blast-2.2.26-x64-linux.t...
}}
***psipred [#mdeea381]
#code(nonumber){{
[root@centos7 ~]# cd /apps/
[root@centos7 apps]# git clone https://github.com/psipred...
[root@centos7 apps]# cd psipred
[root@centos7 psipred]# git checkout -b 4.0 refs/tags/v4.0
Switched to a new branch '4.0'
[root@centos7 psipred]# cd src
[root@centos7 src]# make && make install
[root@centos7 src]# cd /apps/psipred/
[root@centos7 psipred]#
[root@centos7 psipred]# ls -CF
bin/ BLAST+/ data/ example/ LICENSE README runpsipr...
[root@centos7 psipred]#
[root@centos7 psipred]# ls -l bin/
total 68
-rwxr-xr-x. 1 root root 13736 Jan 29 01:45 chkparse
-rwxr-xr-x. 1 root root 18240 Jan 29 01:45 psipass2
-rwxr-xr-x. 1 root root 13744 Jan 29 01:45 psipred
-rwxr-xr-x. 1 root root 13464 Jan 29 01:45 seq2mtx
[root@centos7 psipred]#
}}
***HHSuite [#o802b776]
#code(nonumber){{
[root@centos7 ~]# cd /apps/src
[root@centos7 src]# git clone https://github.com/soeding...
[root@centos7 src]# cd hh-suite/
[root@centos7 hh-suite]# git checkout -b 3.3.0 refs/tags/...
Switched to a new branch '3.3.0'
[root@centos7 hh-suite]#
[root@centos7 hh-suite]# mkdir build && cd $_
[root@centos7 build]# module load mpi/openmpi-x86_64
[root@centos7 build]# cmake -DCMAKE_INSTALL_PREFIX=/apps/...
[root@centos7 build]# make && make install
[root@centos7 build]# ls -l /apps/hh-suite/3.3/
total 8
drwxr-xr-x. 2 root root 4096 Jan 29 01:33 bin
drwxr-xr-x. 2 root root 167 Jan 29 01:33 data
drwxr-xr-x. 2 root root 4096 Jan 29 01:33 scripts
[root@centos7 build]#
}}
設定
#code(nonumber){{
[root@centos7 ~]# vi /apps/hh-suite/3.3/scripts/HHPaths.pm
}}
#code(diff,nonumber){{
--- /apps/hh-suite/3.3/scripts/HHPaths.pm.orig 2021-02-0...
+++ /apps/hh-suite/3.3/scripts/HHPaths.pm 2021-02-0...
@@ -38,18 +38,18 @@
#our $execdir = ".../psipred/bin"; # path to PSI...
#our $datadir = ".../psipred/data"; # path to PSI...
#our $ncbidir = ".../blast/bin"; # path to NCB...
-our $execdir = "/cluster/toolkit/production/bioprogs/psi...
-our $datadir = "/cluster/toolkit/production/bioprogs/psi...
-our $ncbidir = "/cluster/toolkit/production/bioprogs/bla...
+our $execdir = "/apps/psipred/bin"; # path to PSIPRED V...
+our $datadir = "/apps/psipred/data"; # path to PSIPRED V...
+our $ncbidir = "/apps/blast-2.2.26/bin"; # path to NC...
########################################################...
# PLEASE COMPLETE THE PATHS ... TO YOUR LOCAL PDB FILES,...
#our $pdbdir = ".../pdb/all"; # where are t...
#our $dsspdir = ".../dssp/data"; # where are t...
#our $dssp = ".../dssp/bin/dsspcmbi"; # where is th...
-our $pdbdir = "/cluster/databases/pdb/all"; ...
-our $dsspdir = "/cluster/databases/dssp/data"; ...
-our $dssp = "/cluster/databases/dssp/bin/dsspcmbi"; ...
+our $pdbdir = "/Public/databases/pdb/divided"; ...
+our $dsspdir = "/Public/databases/dssp/data"; ...
+our $dssp = "/usr/bin/mkdssp"; # where is the dssp ...
########################################################...
# The lines below probably do not need to be changed
}}
***PDBファイル/DSSPデータベース/HH-suiteデータファイルの...
保存場所の確保
#code(nonumber){{
[root@centos7 ~]# mkdir /Public
[root@centos7 ~]# mount -t nfs qnap:/Public /Public
[root@centos7 ~]# mkdir -p /Public/databases/pdb/divided ...
}}
-PDBファイルの取得
#code(nonumber){{
[root@centos7 ~]# cd /Public/databases/pdb/divided
[root@centos7 divided]# rsync -avz --delete ftp.pdbj.org:...
[root@centos7 divided]# du -hs .
34G .
[root@centos7 divided]# find . -name *.ent.gz -exec /usr/...
}}
解凍前が34GBで解凍すると176GB. 解凍前のファイルはそのまま...
-DSSPデータベースの取得
「rsync://rsync.cmbi.umcn.nl/dssp-from-mmcif/」を参照元に...
#code(nonumber){{
[root@centos7 ~]# rsync -avz --delete rsync://rsync.cmbi....
[root@centos7 ~]# du -hs /Public/databases/dssp/
29G /Public/databases/dssp/
[root@centos7 ~]#
[root@centos7 ~]# ls -l /Public/databases/dssp/data | wc -l
169765
[root@centos7 ~]#
[root@centos7 ~]# find /Public/databases/dssp/data -name ...
169764
[root@centos7 ~]#
}}
だいたい29GBになります. こちらは平文. 総数は 169,764枚
-HH-suite向けのデータファイルを取得
[[http://wwwuser.gwdg.de/~compbiol/uniclust/>+http://wwwu...
#code(nonumber){{
[root@centos7 ~]# cd /Public/databases/HH-suite
[root@centos7 HH-suite]# wget http://wwwuser.gwdg.de/~com...
[root@centos7 HH-suite]# tar xzf UniRef30_2020_06_hhsuite...
[root@centos7 HH-suite]# ls -lh
total 228G
-rw-------. 1 528745 47148 140G Oct 5 21:17 UniRef30_202...
-rw-------. 1 528745 47148 671M Oct 5 21:17 UniRef30_202...
-rw-------. 1 528745 47148 6.0G Oct 5 21:13 UniRef30_202...
-rw-------. 1 528745 47148 605M Oct 5 21:14 UniRef30_202...
-rw-------. 1 528745 47148 35G Oct 5 21:18 UniRef30_202...
-rw-------. 1 528745 47148 20M Oct 5 21:18 UniRef30_202...
-rw-r--r--. 1 root root 47G Feb 1 05:20 UniRef30_202...
-rw-------. 1 528745 47148 379 Oct 7 02:26 UniRef30_202...
[root@centos7 HH-suite]# chmod 644 ./*
[root@centos7 HH-suite]# du -hs .
228G .
[root@centos7 HH-suite]#
}}
176GB＋29GB＋228GB = 433GB
***pyenv/anaconda環境 [#zf8e21f9]
#code(nonumber){{
[root@centos7 ~]# git clone https://github.com/yyuu/pyenv...
[root@centos7 ~]# export PYENV_ROOT=/apps/pyenv
[root@centos7 ~]# export PATH=$PYENV_ROOT/bin:$PATH
[root@centos7 ~]# eval "$(pyenv init - --no-rehash)"
[root@centos7 ~]# pyenv install anaconda3-5.3.1
[root@centos7 ~]# pyenv global anaconda3-5.3.1
[root@centos7 ~]# export PATH=$PYENV_ROOT/versions/anacon...
[root@centos7 ~]# conda update conda
[root@centos7 ~]# conda create -n RaptorX python=2
[root@centos7 ~]# source activate RaptorX
(RaptorX) [root@centos7 ~]# which python2.7
/apps/pyenv/versions/anaconda3-5.3.1/envs/RaptorX/bin/pyt...
(RaptorX) [root@centos7 ~]# conda install numpy nose
(RaptorX) [root@centos7 ~]# conda install -c anaconda msg...
(RaptorX) [root@centos7 ~]# pip install biopython==1.76
(RaptorX) [root@centos7 ~]# conda install pillow
(RaptorX) [root@centos7 ~]# conda install numpy scipy mkl
(RaptorX) [root@centos7 ~]# conda install theano pygpu
(RaptorX) [root@centos7 ~]# mkdir -p /apps/src && cd $_
(RaptorX) [root@centos7 src]# git clone https://github.co...
(RaptorX) [root@centos7 src]# cd shared_ndarray/
(RaptorX) [root@centos7 shared_ndarray]# python2.7 setup....
(RaptorX) [root@centos7 ~]# cd /apps/src
(RaptorX) [root@centos7 src]# tar jxvf PyRosetta4.Release...
(RaptorX) [root@centos7 src]# mv PyRosetta4.Release.pytho...
(RaptorX) [root@centos7 src]# cd PyRosetta4_python27_274/...
(RaptorX) [root@centos7 setup]# python setup.py build
(RaptorX) [root@centos7 setup]# python setup.py install
(RaptorX) [root@centos7 ~]# cd /apps
(RaptorX) [root@centos7 apps]# git clone https://github.c...
(RaptorX) [root@centos7 apps]# cd RaptorX-3DModeling
(RaptorX) [root@centos7 RaptorX-3DModeling]# vi raptorx-e...
}}
#code(diff,nonumber){{
--- /apps/RaptorX-3DModeling/raptorx-external.sh.orig 2...
+++ /apps/RaptorX-3DModeling/raptorx-external.sh 2...
@@ -1,9 +1,9 @@
## the install folder of the hhsuite package, needed for...
-export HHDIR=/mnt/data/RaptorXCommon/HHblits/hhsuite-3.2...
+export HHDIR=/apps/hh-suite/3.3
export PATH=$HHDIR/bin:$HHDIR/scripts:$PATH
## the location of the HHM database to be searched by HH...
-export HHDB=/mnt/data/RaptorXCommon/HHblits/DB/uniref30_...
+export HHDB=/Public/databases/HH-suite/UniRef30_2020_06
## the location of the metagenome data file to be search...
export MetaDB=/mnt/data/conmod_databases/metaclust_serie...
}}
#code(nonumber){{
(RaptorX) [root@centos7 ~]# export ModelingHome=/apps/Rap...
}}
「http://raptorx.uchicago.edu/download/」にて登録を行い「...
#code(nonumber){{
(RaptorX) [root@centos7 ~]# cd $ModelingHome/DL4DistanceP...
(RaptorX) [root@centos7 DL4DistancePrediction4]# tar xf /...
(RaptorX) [root@centos7 DL4DistancePrediction4]# cd $Mode...
(RaptorX) [root@centos7 DL4PropertyPrediction]# tar xf /a...
}}
***HH-Suiteのテスト [#z2a4ba75]
#code(nonumber){{
[illya@centos7 ~]$ mkdir test && cd $_
[illya@centos7 test]$ cp /apps/src/hh-suite/data/query.se...
[illya@centos7 test]$ cat query.seq
>sp|Q5VUD6|FA69B_HUMAN Protein FAM69B OS=Homo sapiens GN=...
MRRLRRLAHLVLFCPFSKRLQGRLPGLRVRCIFLAWLGVFAGSWLVYVHYSSYSERC...
RDKDVTIKCGIEETLDSKARSDAAPRRELVLFDKPTRGTSIKEFREMTLSFLKANLG...
HASRLLGYCGDLYLTEGVPHGAWHAAALPPLLRPLLPPALQGALQQWLGPAWPWRAK...
VRRFLQGRRCEHSTDCTYGRDCRAPCDRLMRQCKGDLIQPNLAKVCALLRGYLLPGA...
[illya@centos7 test]$ /apps/hh-suite/3.3/bin/hhblits -cpu...
- 12:20:21.914 INFO: Search results will be written to qu...
- 12:20:21.914 INFO: Search results will be written to qu...
- 12:20:38.622 INFO: Searching 25985124 column state sequ...
- 12:20:38.675 INFO: query.seq is in A2M, A3M or FASTA fo...
- 12:20:38.675 INFO: Iteration 1
- 12:20:38.867 INFO: Prefiltering database
- 12:22:00.098 INFO: HMMs passed 1st prefilter (gapless p...
- 12:22:02.105 INFO: HMMs passed 2nd prefilter (gapped pr...
- 12:22:02.105 INFO: HMMs passed 2nd prefilter and not fo...
- 12:22:02.105 INFO: Scoring 419 HMMs using HMM-HMM Viter...
- 12:22:02.299 INFO: Alternative alignment: 0
- 12:22:23.947 INFO: 419 alignments done
- 12:22:23.948 INFO: Alternative alignment: 1
- 12:22:24.044 INFO: 415 alignments done
- 12:22:24.045 INFO: Alternative alignment: 2
- 12:22:24.075 INFO: 56 alignments done
- 12:22:24.075 INFO: Alternative alignment: 3
- 12:22:24.087 INFO: 4 alignments done
- 12:22:25.010 INFO: Premerge done
- 12:22:25.011 INFO: Realigning 318 HMM-HMM alignments us...
- 12:22:26.674 INFO: 94 sequences belonging to 94 databas...
- 12:22:26.674 INFO: Number of effective sequences of res...
Query sp|Q5VUD6|FA69B_HUMAN Protein FAM69B OS=Hom...
Match_columns 431
No_of_seqs 520 out of 780
Neff 6.52866
Searched_HMMs 419
Date Tue Feb 2 12:22:26 2021
Command /apps/hh-suite/3.3/bin/hhblits -cpu 4 -i qu...
No Hit Prob E-value P-value ...
1 UniRef100_A0A024R8I5 Family wi 100.0 2E-172 5E-178 ...
2 UniRef100_UPI000C879985 protei 100.0 4E-160 9E-166 ...
:
[illya@centos7 test]$
}}
***RaptorX-3DModeling [#u294b1b7]
テスト
参照元と同じく2O6Pで
#code(nonumber){{
[illya@centos7 ~]$ cd test
[illya@centos7 test]$ vi 2o6pA.fasta
>2O6P_1|Chains A,B|Iron-regulated surface determinant pro...
NAADSGTLNYEVYKYNTNDTSIANDYFNKPAKYIKKNGKLYVQITVNHSHWITGMSI...
TYKFNGPTDVAGAN
[illya@centos7 test]$
[illya@centos7 test]$ export PYENV_ROOT=/apps/pyenv
[illya@centos7 test]$ export PATH=$PYENV_ROOT/bin:$PATH
[illya@centos7 test]$ eval "$(pyenv init - --no-rehash)"
[illya@centos7 test]$ export PATH=$PYENV_ROOT/versions/an...
[illya@centos7 test]$ export CUDA_ROOT=/usr/local/cuda-10.2
[illya@centos7 test]$ source activate RaptorX
(RaptorX) [illya@centos7 test]$
(RaptorX) [illya@centos7 test]$ export ModelingHome=/apps...
(RaptorX) [illya@centos7 test]$ . $ModelingHome/raptorx-p...
(RaptorX) [illya@centos7 test]$ . $ModelingHome/raptorx-e...
(RaptorX) [illya@centos7 test]$ /apps/RaptorX-3DModeling/...
(略)/RaptorXFolder.sh [ -o outDir | -g gpu | -m MSAmethod...
This script predicts angle/contact/distance/orien...
ModelingHome=/apps/RaptorX-3DModeling
Please make sure that ModelingHome is cor...
Before running this script, some external...
inputFile: a protein primary sequence file in FAS...
:
:
(RaptorX) [illya@centos7 test]$ /apps/RaptorX-3DModeling/...
}}
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