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#author("2021-02-03T15:55:56+00:00","default:sysosa","sysosa") #author("2021-02-03T16:06:12+00:00","default:sysosa","sysosa") 本家様[[http://raptorx.uchicago.edu/>+http://raptorx.uchicago.edu/]] [[https://github.com/j3xugit/RaptorX-3DModeling>+https://github.com/j3xugit/RaptorX-3DModeling]] 参照先[[https://qiita.com/Ag_smith/items/9e6a29faa719be64be90>+https://qiita.com/Ag_smith/items/9e6a29faa719be64be90]] ***下準備 [#a5013d2f] #code(nonumber){{ yum install epel-release yum install cmake python3 openmpi-devel dssp screen wget parallel mkdir -p /apps/src }} #code(nonumber){{ yum localinstall cuda-repo-rhel7-11-2-local-11.2.0_460.27.04-1.x86_64.rpm yum install cuda-11-2 yum localinstall cuda-repo-rhel7-10-2-local-10.2.89-440.33.01-1.0-1.x86_64.rpm yum install yum install cuda-libraries-dev-10-2 yum remove "cuda-repo*" }} cuda-11.2, cuda-10.2 インストール済み #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-10.2/ }} 「site-packages/theano/gpuarray/dnn.py」から「cuDNN to a version >= v5 and <= v7」と言われるが、 dnn.pyを調べると「v >= 7200:」と要求される cudnnは 7.2未満？ &size(10){「site-packages/theano/gpuarray/dnn.py」から「cuDNN to a version >= v5 and <= v7」と言われるが、dnn.pyを調べると「v >= 7200:」と要求される cudnnは 7.2未満？}; &size(10){カードの問題なのか不明だが、10.2ではGPUで計算出来ていない.}; ***pdbx [#c59b86c9] #code(nonumber){{ [root@centos7 ~]# cd /apps/ [root@centos7 apps]# git clone https://github.com/soedinglab/pdbx [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-packages/pdbx」にインストールされる ***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/blast/executables/legacy.NOTSUPPORTED/2.2.26/blast-2.2.26-x64-linux.tar.gz [root@centos7 src]# cd .. [root@centos7 apps]# tar xzf src/blast-2.2.26-x64-linux.tar.gz }} ***psipred [#mdeea381] #code(nonumber){{ [root@centos7 ~]# cd /apps/ [root@centos7 apps]# git clone https://github.com/psipred/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 runpsipred* runpsipred_single* src/ VERSION [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/soedinglab/hh-suite [root@centos7 src]# cd hh-suite/ [root@centos7 hh-suite]# git checkout -b 3.3.0 refs/tags/v3.3.0 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/hh-suite/3.3 .. [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 2021-02-02 10:26:41.000000000 +0900 +++ /apps/hh-suite/3.3/scripts/HHPaths.pm 2021-02-02 10:33:49.738884533 +0900 @@ -38,18 +38,18 @@ #our $execdir = ".../psipred/bin"; # path to PSIPRED V2 binaries #our $datadir = ".../psipred/data"; # path to PSIPRED V2 data files #our $ncbidir = ".../blast/bin"; # path to NCBI binaries (for PSIPRED in addss.pl) -our $execdir = "/cluster/toolkit/production/bioprogs/psipred/bin"; # path to PSIPRED V2 binaries -our $datadir = "/cluster/toolkit/production/bioprogs/psipred/data"; # path to PSIPRED V2 data files -our $ncbidir = "/cluster/toolkit/production/bioprogs/blast/bin"; # path to NCBI binaries (for PSIPRED in addss.pl) +our $execdir = "/apps/psipred/bin"; # path to PSIPRED V2 binaries +our $datadir = "/apps/psipred/data"; # path to PSIPRED V2 data files +our $ncbidir = "/apps/blast-2.2.26/bin"; # path to NCBI binaries (for PSIPRED in addss.pl) ############################################################################################## # PLEASE COMPLETE THE PATHS ... TO YOUR LOCAL PDB FILES, DSSP FILES ETC. #our $pdbdir = ".../pdb/all"; # where are the pdb files? (pdb/divided directory will also work) #our $dsspdir = ".../dssp/data"; # where are the dssp files? Used in addss.pl. #our $dssp = ".../dssp/bin/dsspcmbi"; # where is the dssp binary? Used in addss.pl. -our $pdbdir = "/cluster/databases/pdb/all"; # where are the pdb files? (pdb/divided directory will also work) -our $dsspdir = "/cluster/databases/dssp/data"; # where are the dssp files? Used in addss.pl -our $dssp = "/cluster/databases/dssp/bin/dsspcmbi"; # where is the dssp binary? Used in addss.pl +our $pdbdir = "/Public/databases/pdb/divided"; # where are the pdb files? (pdb/divided directory will also work) +our $dsspdir = "/Public/databases/dssp/data"; # where are the dssp files? Used in addss.pl +our $dssp = "/usr/bin/mkdssp"; # where is the dssp binary? Used in addss.pl ############################################################################################## # The lines below probably do not need to be changed }} ***PDBファイル/DSSPデータベース/HH-suiteデータファイルの取得 [#dad7f27e] 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 /Public/databases/dssp/data /Public/databases/HH-suite }} -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::ftp_data/structures/divided/pdb . [root@centos7 divided]# du -hs . 34G . [root@centos7 divided]# find . -name *.ent.gz -exec /usr/local/bin/gzip -dk {} \; # gzip-1.10を/usr/local/binにインスト }} 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にしているので、正味 142GBでしょうか -DSSPデータベースの取得 「rsync://rsync.cmbi.umcn.nl/dssp-from-mmcif/」を参照元にしたら多くのファイルで「&color(red){rsync: send_files failed to open "/6yt9.dssp" (in dssp-from-mmcif): Permission denied (13)};」とエラーが表示された. なので別の取得先に変更 #code(nonumber){{ [root@centos7 ~]# rsync -avz --delete rsync://rsync.cmbi.umcn.nl/dssp/ /Public/databases/dssp/data/ [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 *.dssp | wc -l 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://wwwuser.gwdg.de/~compbiol/uniclust/]] #code(nonumber){{ [root@centos7 ~]# cd /Public/databases/HH-suite [root@centos7 HH-suite]# wget http://wwwuser.gwdg.de/~compbiol/uniclust/2020_06/UniRef30_2020_06_hhsuite.tar.gz [root@centos7 HH-suite]# tar xzf UniRef30_2020_06_hhsuite.tar.gz [root@centos7 HH-suite]# ls -lh total 228G -rw-------. 1 528745 47148 140G Oct 5 21:17 UniRef30_2020_06_a3m.ffdata -rw-------. 1 528745 47148 671M Oct 5 21:17 UniRef30_2020_06_a3m.ffindex -rw-------. 1 528745 47148 6.0G Oct 5 21:13 UniRef30_2020_06_cs219.ffdata -rw-------. 1 528745 47148 605M Oct 5 21:14 UniRef30_2020_06_cs219.ffindex -rw-------. 1 528745 47148 35G Oct 5 21:18 UniRef30_2020_06_hhm.ffdata -rw-------. 1 528745 47148 20M Oct 5 21:18 UniRef30_2020_06_hhm.ffindex -rw-r--r--. 1 root root 47G Feb 1 05:20 UniRef30_2020_06_hhsuite.tar.gz -rw-------. 1 528745 47148 379 Oct 7 02:26 UniRef30_2020_06.md5sums [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.git /apps/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=$PYENV_ROOT/versions/anaconda3-5.3.1/bin/:$PATH [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/python2.7 (RaptorX) [root@centos7 ~]# conda install numpy nose (RaptorX) [root@centos7 ~]# conda install -c anaconda msgpack-python (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 $_ (RaptorX) [root@centos7 src]# git clone https://github.com/crowsonkb/shared_ndarray.git (RaptorX) [root@centos7 src]# cd shared_ndarray/ (RaptorX) [root@centos7 shared_ndarray]# python2.7 setup.py install (RaptorX) [root@centos7 ~]# cd /apps/src (RaptorX) [root@centos7 src]# tar jxvf PyRosetta4.Release.python27.linux.release-274.tar.bz2 (RaptorX) [root@centos7 src]# mv PyRosetta4.Release.python27.linux.release-274 PyRosetta4_python27_274 (RaptorX) [root@centos7 src]# cd PyRosetta4_python27_274/setup/ (RaptorX) [root@centos7 setup]# python setup.py build (RaptorX) [root@centos7 setup]# python setup.py install (RaptorX) [root@centos7 ~]# cd /apps (RaptorX) [root@centos7 apps]# git clone https://github.com/j3xugit/RaptorX-3DModeling.git (RaptorX) [root@centos7 apps]# cd RaptorX-3DModeling (RaptorX) [root@centos7 RaptorX-3DModeling]# vi raptorx-external.sh }} #code(diff,nonumber){{ --- /apps/RaptorX-3DModeling/raptorx-external.sh.orig 2021-02-02 09:29:21.529937627 +0900 +++ /apps/RaptorX-3DModeling/raptorx-external.sh 2021-02-02 14:20:13.065802041 +0900 @@ -1,9 +1,9 @@ ## the install folder of the hhsuite package, needed for MSA generation. -export HHDIR=/mnt/data/RaptorXCommon/HHblits/hhsuite-3.2.0-SSE2-Linux/ +export HHDIR=/apps/hh-suite/3.3 export PATH=$HHDIR/bin:$HHDIR/scripts:$PATH ## the location of the HHM database to be searched by HHblits for MSA generation. Needed unless you already have an MSA and do not want to generate any new MSAs. -export HHDB=/mnt/data/RaptorXCommon/HHblits/DB/uniref30_2020_02/UniRef30_2020_02 +export HHDB=/Public/databases/HH-suite/UniRef30_2020_06 ## the location of the metagenome data file to be searched by hmmsearch. Not needed unless you want to build MSAs using metagenome data. export MetaDB=/mnt/data/conmod_databases/metaclust_series/metaclust_50.fasta }} #code(nonumber){{ (RaptorX) [root@centos7 ~]# export ModelingHome=/apps/RaptorX-3DModeling }} 「http://raptorx.uchicago.edu/download/」にて登録を行い「RXDeepModels4DistOri-FM.tar.gz」と「RXDeepModels4Property.tar.gz」を得る #code(nonumber){{ (RaptorX) [root@centos7 ~]# cd $ModelingHome/DL4DistancePrediction4 (RaptorX) [root@centos7 DL4DistancePrediction4]# tar xf /apps/src/RXDeepModels4DistOri-FM.tar.gz (RaptorX) [root@centos7 DL4DistancePrediction4]# cd $ModelingHome/DL4PropertyPrediction (RaptorX) [root@centos7 DL4PropertyPrediction]# tar xf /apps/src/RXDeepModels4Property.tar.gz }} ***HH-Suiteのテスト [#z2a4ba75] #code(nonumber){{ [illya@centos7 ~]$ mkdir test && cd $_ [illya@centos7 test]$ cp /apps/src/hh-suite/data/query.seq . [illya@centos7 test]$ cat query.seq >sp|Q5VUD6|FA69B_HUMAN Protein FAM69B OS=Homo sapiens GN=FAM69B PE=2 SV=3 MRRLRRLAHLVLFCPFSKRLQGRLPGLRVRCIFLAWLGVFAGSWLVYVHYSSYSERCRGHVCQVVICDQYRKGIISGSVCQDLCELHMVEWRTCLSVAPGQQVYSGLW RDKDVTIKCGIEETLDSKARSDAAPRRELVLFDKPTRGTSIKEFREMTLSFLKANLGDLPSLPALVGQVLLMADFNKDNRVSLAEAKSVWALLQRNEFLLLLSLQEKE HASRLLGYCGDLYLTEGVPHGAWHAAALPPLLRPLLPPALQGALQQWLGPAWPWRAKIAIGLLEFVEELFHGSYGTFYMCETTLANVGYTATYDFKMADLQQVAPEAT VRRFLQGRRCEHSTDCTYGRDCRAPCDRLMRQCKGDLIQPNLAKVCALLRGYLLPGAPADLREELGTQLRTCTTLSGLASQVEAHHSLVLSHLKTLLWKKISNTKYS [illya@centos7 test]$ /apps/hh-suite/3.3/bin/hhblits -cpu 4 -i query.seq -d /Public/databases/HH-suite/UniRef30_2020_06 -oa3m query.a3m -n -1 - 12:20:21.914 INFO: Search results will be written to query.hhr - 12:20:21.914 INFO: Search results will be written to query.hhr - 12:20:38.622 INFO: Searching 25985124 column state sequences. - 12:20:38.675 INFO: query.seq is in A2M, A3M or FASTA format - 12:20:38.675 INFO: Iteration 1 - 12:20:38.867 INFO: Prefiltering database - 12:22:00.098 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment) : 616605 - 12:22:02.105 INFO: HMMs passed 2nd prefilter (gapped profile-profile alignment) : 419 - 12:22:02.105 INFO: HMMs passed 2nd prefilter and not found in previous iterations : 419 - 12:22:02.105 INFO: Scoring 419 HMMs using HMM-HMM Viterbi alignment - 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 using Maximum Accuracy algorithm - 12:22:26.674 INFO: 94 sequences belonging to 94 database HMMs found with an E-value < 0.001 - 12:22:26.674 INFO: Number of effective sequences of resulting query HMM: Neff = 6.52866 Query sp|Q5VUD6|FA69B_HUMAN Protein FAM69B OS=Homo sapiens GN=FAM69B PE=2 SV=3 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 query.seq -d /Public/databases/HH-suite/UniRef30_2020_06 -oa3m query.a3m -n -1 No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 UniRef100_A0A024R8I5 Family wi 100.0 2E-172 5E-178 1290.6 0.0 431 1-431 240-670 (762) 2 UniRef100_UPI000C879985 protei 100.0 4E-160 9E-166 1176.4 0.0 412 20-431 235-767 (767) : [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 protein C|Staphylococcus aureus subsp. aureus (158879) NAADSGTLNYEVYKYNTNDTSIANDYFNKPAKYIKKNGKLYVQITVNHSHWITGMSIEGHKENIISKNTAKDERTSEFEVSKLNGKIDGKIDVYIDEKVNGKPFKYDHHYNI 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=$PYENV_ROOT/versions/anaconda3-5.3.1/bin/:$PATH [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-3DModeling (RaptorX) [illya@centos7 test]$ . $ModelingHome/raptorx-path.sh (RaptorX) [illya@centos7 test]$ . $ModelingHome/raptorx-external.sh (RaptorX) [illya@centos7 test]$ /apps/RaptorX-3DModeling/Server/RaptorXFolder.sh (略)/RaptorXFolder.sh [ -o outDir | -g gpu | -m MSAmethod | -n numDecoys | -r runningMode | -R remoteAccountInfo | -t machineType | -l maxLen2BeFolded | -c ] inputFile This script predicts angle/contact/distance/orientation of a protein and optionally folds it ModelingHome=/apps/RaptorX-3DModeling Please make sure that ModelingHome is correctly set to the install folder of the RaptorX-3DModeling package Before running this script, some external software packages shall be installed. See README.md for instructions. inputFile: a protein primary sequence file in FASTA format (ending with .fasta or .seq) or a multiple sequence alignment file in a3m format (ending with .a3m) : : (RaptorX) [illya@centos7 test]$ /apps/RaptorX-3DModeling/Server/RaptorXFolder.sh -g -1 -l 1050 -m 9 -n 20 -r 1 -t 1 2o6pA.fasta }}
