# blast-gpu-10-1
cuda10.1
#一键安装
```
docker run --name blast_项目名称 -it napoler/docker_gpu_bast:10.1 bash
```
# 测试不保存
docker run --rm -it blast-gpu-10-1:latest bash
# 长期使用
docker run --name blast_项目名称 -it blast-gpu-10-1:latest bash
# 程序目录
/ncbi-blast-2.2.28+-src/c++/GCC485-ReleaseMT64/bin/blastp
************************ GPU-BLAST 1.1 [February 2016] ************************
GPU-BLAST is designed to accelerate the gapped and ungapped protein sequence
alignment algorithms of the NCBI-BLAST implementation. GPU-BLAST is integrated
into the NCBI-BLAST code and produces identical results. It has been tested
on CentOS 5.5, 6.7, 7.2 and Fedora 10 with an NVIDIA Tesla C1060, an NVIDIA
Tesla C2050 and an NVIDIA Tesla K40 GPU.
GPU-BLAST is free software.
Please cite the authors in any work or product based on this material:
Panagiotis D. Vouzis and Nikolaos V. Sahinidis, "GPU-BLAST: Using graphics
processors to accelerate protein sequence alignment," Vol. 27, no. 2,
pages 182-188, Bioinformatics, 2011 (Open Access).
For any questions and feedback about GPU-BLAST, contact sahinidis@cmu.edu.
I. Supported features
=====================
GPU-BLAST 1.1 supports protein alignment and is integrated in the "blastp"
executable produced after installation. GPU-BLAST 1.1 does not support
PSI BLAST.
II. Installation instructions
=============================
GPU-BLAST modifies NCBI-BLAST in order to add GPU functionality. These
modifications do not alter the standard NCBI-BLAST when the GPU is not used.
In addition, the results of GPU-BLAST are identical to those from NCBI-BLAST,
irrespective of whether the GPU is used for calculations or not.
GPU-BLAST has been developed and tested on NVIDIA GPUs Tesla C1060, C2050 and
K40. The present version requires a CUDA-capable NVIDIA GPU and the CUDA nvcc
compiler.
The following sequence of commands are on a CentOS 7.2 with CUDA 7.5 and gcc
v4.8.2.
The login shell is bash.
The installation files are placed on an existing folder named "blast".
There are two possible ways to install GPU-BLAST: (i) install NCBI-BLAST and
add GPU-BLAST later (Option 1), or (ii) directly install NCBI-BLAST and GPU-BLAST
(Option 2).
Option 1: Install NCBI-BLAST (maybe it is already installed) and add GPU-BLAST later
If you want to directly install both NCBI-BLAST and GPU-BLAST skip to option 2.
Step 1. NCBI-BLAST installation
If you have already installed NCBI-BLAST, go to step 2.
[ploskas@anaximander blast]$ wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.28/ncbi-blast-2.2.28+-src.tar.gz
--2016-02-09 13:13:32-- ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.28/ncbi-blast-2.2.28+-src.tar.gz
=> �ncbi-blast-2.2.28+-src.tar.gz�
Resolving ftp.ncbi.nlm.nih.gov (ftp.ncbi.nlm.nih.gov)... 130.14.250.7, 2607:f220:41e:250::10
Connecting to ftp.ncbi.nlm.nih.gov (ftp.ncbi.nlm.nih.gov)|130.14.250.7|:21... connected.
Logging in as anonymous ... Logged in!
==> SYST ... done. ==> PWD ... done.
==> TYPE I ... done. ==> CWD (1) /blast/executables/blast+/2.2.28 ... done.
==> SIZE ncbi-blast-2.2.28+-src.tar.gz ... 13468751
==> PASV ... done. ==> RETR ncbi-blast-2.2.28+-src.tar.gz ... done.
Length: 13468751 (13M) (unauthoritative)
100%[====================================================================================>] 13,468,751 3.89MB/s in 3.3s
2016-02-09 13:13:36 (3.89 MB/s) - �ncbi-blast-2.2.28+-src.tar.gz� saved [13468751]
[ploskas@anaximander blast]$ ls
ncbi-blast-2.2.28+-src.tar.gz
[ploskas@anaximander blast]$ tar -xvzf ncbi-blast-2.2.28+-src.tar.gz
[ploskas@anaximander blast]$ rm -r ncbi-blast-2.2.28+-src.tar.gz
[ploskas@anaximander blast]$ ls
ncbi-blast-2.2.28+-src
[ploskas@anaximander blast]$ cd ncbi-blast-2.2.28+-src/c++
[ploskas@anaximander c++]$ ./configure
[ploskas@anaximander c++]$ make
[ploskas@anaximander c++]$ make install
Depending on the version of your gcc compiler, NCBI-BLAST creates a directory inside
"ncbi-blast-2.2.28+-src/c++". For example, if you use gcc v4.8.2 the directory will be
named "GCC482-Debug64". Inside this directory, a directory named "bin" exists where all
the needed executables are placed, e.g. makeblastdb and blastp. Please change accordingly
the name of this folder to the following commands.
Step 2. GPU-BLAST installation
Adding GPU functionality to an existing installation of NCBI-BLAST.
[ploskas@anaximander blast]$ ls
ncbi-blast-2.2.28+-src
[ploskas@anaximander blast]$ wget http://thales.cheme.cmu.edu/gpublast/gpu-blast-1.1_ncbi-blast-2.2.28.tar.gz
--2016-02-09 13:56:41-- http://thales.cheme.cmu.edu/gpublast/gpu-blast-1.1_ncbi-blast-2.2.28.tar.gz
Resolving thales.cheme.cmu.edu (thales.cheme.cmu.edu)... 128.2.55.81
Connecting to thales.cheme.cmu.edu (thales.cheme.cmu.edu)|128.2.55.81|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 252460 (247K) [application/x-gzip]
Saving to: �gpu-blast-1.1_ncbi-blast-2.2.28.tar.gz�
100%[====================================================================================>] 252,460 --.-K/s in 0.02s
2016-02-09 13:56:41 (11.5 MB/s) - �gpu-blast-1.1_ncbi-blast-2.2.28.tar.gz� saved [252460/252460]
[ploskas@anaximander blast]$ ls
gpu-blast-1.1_ncbi-blast-2.2.28.tar.gz ncbi-blast-2.2.28+-src
[ploskas@anaximander blast]$ tar -xzf gpu-blast-1.1_ncbi-blast-2.2.28.tar.gz
[ploskas@anaximander blast]$ rm gpu-blast-1.1_ncbi-blast-2.2.28.tar.gz
[ploskas@anaximander blast]$ ls
gpu_blast install ncbi-blast-2.2.28+-src README
[ploskas@anaximander blast]$ sudo sh ./install
Do you want to install GPU-BLAST on an existing installation of "blastp" [yes/no]
yes: you will be asked for the installation directory of the "blastp" executable
no: will download and install "ncbi-blast-2.2.28+-src"
yes
Please input the installation directory of "blastp" of "ncbi-blast-2.2.28+-src"
/home/ploskas/blast/ncbi-blast-2.2.28+-src/c++/GCC482-Debug64/bin/
"blastp" version 2.2.28+ is compatible
Continuing with the installation of GPU-BLAST...
Modifying NCBI BLAST files
Compiling CUDA code
....
Building NCBI BLAST with GPU BLAST
.................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
Option 2: Directly install both NCBI-BLAST and GPU-BLAST
[ploskas@anaximander blast]$ wget http://thales.cheme.cmu.edu/gpublast/gpu-blast-1.1_ncbi-blast-2.2.28.tar.gz
--2016-02-09 15:15:34-- http://thales.cheme.cmu.edu/gpublast/gpu-blast-1.1_ncbi-blast-2.2.28.tar.gz
Resolving thales.cheme.cmu.edu (thales.cheme.cmu.edu)... 128.2.55.81
Connecting to thales.cheme.cmu.edu (thales.cheme.cmu.edu)|128.2.55.81|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 252460 (247K) [application/x-gzip]
Saving to: �gpu-blast-1.1_ncbi-blast-2.2.28.tar.gz�
100%[====================================================================================>] 252,460 --.-K/s in 0.02s
2016-02-09 15:15:34 (11.8 MB/s) - �gpu-blast-1.1_ncbi-blast-2.2.28.tar.gz� saved [252460/252460]
[ploskas@anaximander blast]$ ls
gpu-blast-1.1_ncbi-blast-2.2.28.tar.gz
[ploskas@anaximander blast]$ tar -xzf gpu-blast-1.1_ncbi-blast-2.2.28.tar.gz
[ploskas@anaximander blast]$ rm gpu-blast-1.1_ncbi-blast-2.2.28.tar.gz
[ploskas@anaximander blast]$ ls
gpu_blast install README
[ploskas@anaximander blast]$ sh ./install
Do you want to install GPU-BLAST on an existing installation of "blastp" [yes/no]
yes: you will be asked for the installation directory of the "blastp" executable
no: will download and install "ncbi-blast-2.2.28+-src"
no
Continuing with the downloading of ncbi-blast-2.2.28+-src...
Downloading NBCI BLAST
--2016-02-09 15:29:18-- ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.28/ncbi-blast-2.2.28+-src.tar.gz
=> �ncbi-blast-2.2.28+-src.tar.gz�
Resolving ftp.ncbi.nlm.nih.gov (ftp.ncbi.nlm.nih.gov)... 130.14.250.11, 2607:f220:41e:250::7
Connecting to ftp.ncbi.nlm.nih.gov (ftp.ncbi.nlm.nih.gov)|130.14.250.11|:21... connected.
Logging in as anonymous ... Logged in!
==> SYST ... done. ==> PWD ... done.
==> TYPE I ... done. ==> CWD (1) /blast/executables/blast+/2.2.28 ... done.
==> SIZE ncbi-blast-2.2.28+-src.tar.gz ... 13468751
==> PASV ... done. ==> RETR ncbi-blast-2.2.28+-src.tar.gz ... done.
Length: 13468751 (13M) (unauthoritative)
100%[====================================================================================>] 13,468,751 8.39MB/s in 1.5s
2016-02-09 15:29:20 (8.39 MB/s) - �ncbi-blast-2.2.28+-src.tar.gz� saved [13468751]
Extracting NCBI BLAST
.
Configuring ncbi-blast-2.2.28+-src with options:
../configure --without-debug --with-mt --without-sybase --without-ftds --without-fastcgi --without-ncbi-c --without-sssdb --without-sss --without-geo --without-sp --without-orbacus --without-boost
If you want to change these options edit the file "install", delete the directory ncbi-blast-2.2.28+-src, and rerun install
...............................
Modifying NCBI BLAST files
Compiling CUDA code
....
Building NCBI BLAST with GPU BLAST
..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
[ploskas@anaximander blast]$ ls
configure.output gpu_blast.output modify.output ncbi-blast-2.2.28+-src.tar.gz README
gpu_blast install ncbi-blast-2.2.28+-src ncbi_blast.output
Depending on the version of your gcc compiler, NCBI-BLAST creates a directory inside
ncbi-blast-2.2.28+-src/c++. For example, if you use gcc v4.8.2 the directory will be
named "GCC482-ReleaseMT64". Inside this directory, a directory named bin exists where all
the needed executables are placed, e.g. makeblastdb and blastp.
NOTE: if you used Option 1 to install GPU-BLAST after installing NCBI-BLAST, the name
of this folder would be "GCC482-Debug64". Please change accordingly the name of this folder
to the following commands.
III. How to use GPU-BLAST
=========================
If the above process is successful, the NCBI-BLAST installed will offer the
additional option of using GPU-BLAST. The interface of GPU-BLAST is identical
to the original NCBI-BLAST interface with the following additional options
for "blastp":
*** GPU options
-gpu <Boolean>
Use GPU for blastp
Default = `F'
-gpu_threads <Integer, 1..1024>
Number of GPU threads per block
Default = `64'
-gpu_blocks <Integer, 1..65536>
Number of GPU block per grid
Default = `512'
-method <Integer, 1..2>
Method to be used
1 = for GPU-based sequence alignment (default),
2 = for GPU database creation
Default = `1'
* Incompatible with: num_threads
Typing "./blastp -help" will print the above options towards the end of the output.
GPU-BLAST also adds the option "-sort_volumes" in the "makeblastdb" executable in
"/ncbi-blast-2.2.28+-src/c++/GCC482-ReleaseMT64/bin". "makeblastdb" is an executable that
formats a FASTA database to the appropriate format to be used by NCBI-BLAST. The option
"-sort_volumes" sorts the database volumes produced according to length.
NOTE: "makeblastdb" has the option to split input databases in chunks, called volumes, according
to the users choice.
When you type "./makeblastdb -help", you will see the additional option listed in
comparison to the original NCBI-BLAST "makeblastdb"
*** Miscellaneous options
-sort_volumes
Sort the sequences according to length in each volume
The following example uses the protein FASTA formatted database, called "env_nr". Create
a directory "database" inside directory "blast" and download the database env_nr inside
this directory.
[ploskas@anaximander blast]$ mkdir database
[ploskas@anaximander blast]$ cd database
[ploskas@anaximander database]$ wget ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/env_nr.gz
[ploskas@anaximander database]$ gunzip env_nr.gz
[ploskas@anaximander database]$ rm enc_nr.gz
Then, create a directory "queries" inside directory "blast" and download some sample
queries inside this folder.
[ploskas@anaximander blast]$ cd ..
[ploskas@anaximander blast]$ mkdir queries
[ploskas@anaximander blast]$ cd queries
[ploskas@anaximander queries]$ wget http://thales.cheme.cmu.edu/gpublast/queries.tar.gz
[ploskas@anaximander database]$ tar -xzf queries.tar.gz
[ploskas@anaximander database]$ rm queries.tar.gz
The tree structure of the folder "blast" should look like:
blast
|-- database
| |-- env_nr
|-- gpublast
| |-- ncbi_blast_files
| | -- .
| | -- .
| | -- .
| |-- gpu_blastp.c
| |-- .
| |-- .
| |-- .
|-- ncbi-blast-2.2.28+-src/
| |-- c++
| | |-- compilers
| | | |-- .
| | | |-- .
| | | |-- .
| | |-- GCC482-ReleaseMT64
| | | |-- bin
| | | | |-- blastp
| | | | |-- makeblastdb
| | | | |-- .
| | | | |-- .
| | | | |-- .
| | | |-- build
| | | | |-- .
| | | | |-- .
| | | | |-- .
| | | |-- inc
| | | | |-- .
| | | | |-- .
| | | | |-- .
| | | |-- lib
| | | | |-- .
| | | | |-- .
| | | | |-- .
| | | |-- status
| | | | |-- .
| | | | |-- .
| | | | |-- .
| | |-- include
| | | |-- .
| | | |-- .
| | | |-- .
| | |-- scripts
| | | |-- .
| | | |-- .
| | | |-- .
| | |-- src
| | | |-- .
| | | |-- .
| | | |-- .
| | |-- config.log
| | |-- configure
| | |-- Makefile
|-- queries
| |-- SequenceLength_00000002.txt
| |-- .
| |-- .
| |-- .
| |-- SequenceLength_00004998.txt
|-- install
|-- README
To use GPU-BLAST, first sort the protein database according to sequence length,
create a database for the GPU and execute blastp on the GPU.
Step 1. Sorting a database
To sort a database use the option "-sort_volumes" with "makeblastdb".
"-sort_volumes" works only with protein FASTA-formatted databases. Assuming
the database "env_nr" is saved in the directory "/blast/database", type:
[ploskas@anaximander blast]$ cd ncbi-blast-2.2.28+-src/c++/GCC482-ReleaseMT64/bin/
[ploskas@anaximander bin]$ ./makeblastdb -in ../../../../database/env_nr -out ../../../../database/sorted_env_nr -dbtype prot -sort_volumes -max_file_sz 500MB
Building a new DB, current time: 02/09/2016 16:16:57
New DB name: ../../../../database/sorted_env_nr
New DB title: ../../../../database/env_nr
Sequence type: Protein
Keep Linkouts: T
Keep MBits: T
Maximum file size: 500000000B
Sorting 2676410 sequences
Writing to Volume
Done Writing to Database
Sorting 2677316 sequences
Writing to Volume
Done Writing to Database
Adding sequences from FASTA; added 6031291 sequences in 267.507 seconds.
Sorting 677565 sequences
Writing to Volume
Done Writing to Database
This will produce the following files inside the database directory:
[ploskas@anaximander bin]$ ls ../../../../database
env_nr sorted_env_nr.00.phr sorted_env_nr.00.pin sorted_env_nr.00.psq sorted_env_nr.01.phr sorted_env_nr.01.pin sorted_env_nr.01.psq sorted_env_nr.02.phr sorted_env_nr.02.pin sorted_env_nr.02.psq sorted_env_nr.pal
Since this process only sorts the database, the "sorted_env_nr" will produce
identical alignments with the original "env_nr", no matter whether GPU-BLAST
is used or not.
NOTE: By using the option "-sort_volumes", "makeblastdb" stores in a vector each
volume of the produced database in order to sort it. This may require large amounts
of memory, depending on the database size and the options used with "makeblastdb".
If, by using "-sort_volumes", the program runs out of memory, consider using the
option "-max_file_sz" to produce smaller database volumes compared to the default
NCBI size which is 1 GB.
"./makeblastdb -in ../../../../database/env_nr -out ../../../../database/sorted_env_nr
-dbtype prot -sort_volumes -max_file_sz 200MB"
to produce database volumes with size up to 200 MB.
Step 2. Creating a GPU database
To create the database in the appropriate GPU-BLAST format from the sorted
database created in the previous step, treat the sorted database as any database
that you would use to align a sequence against; i.e., format and sort the input
database with "makeblastdb" (see step 1). Then, execute "./blastp" with the added
options "-gpu T -method 2 -gpu_blocks <Integer, 1..65536> -gpu_threads <Integer, 1..1024>".
For example, to create a database for GPU-BLAST of the "sorted_env_nr", type
[ploskas@anaximander bin]$ ./blastp -query ../../../../queries/SequenceLength_00000100.txt -db ../../../../database/sorted_env_nr -gpu t -method 2 -gpu_blocks 256 -gpu_threads 32
../../../../database/sorted_env_nr.00.pin: 2538598
../../../../database/sorted_env_nr.01.pin: 2614567
../../../../database/sorted_env_nr.02.pin: 1811780
num_volumes = 3
Done with creating the GPU Database file (../../../../database/sorted_env_nr.00.gpu)
Done with creating the GPU Database file (../../../../database/sorted_env_nr.01.gpu)
Done with creating the GPU Database file (../../../../database/sorted_env_nr.02.gpu)
BLASTP 2.2.28+
Reference: Stephen F. Altschul, Thomas L. Madden, Alejandro A.
Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J.
Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of
protein database search programs", Nucleic Acids Res. 25:3389-3402.
Reference for composition-based statistics: Alejandro A. Schaffer,
L. Aravind, Thomas L. Madden, Sergei Shavirin, John L. Spouge, Yuri
I. Wolf, Eugene V. Koonin, and Stephen F. Altschul (2001),
"Improving the accuracy of PSI-BLAST protein database searches with
composition-based statistics and other refinements", Nucleic Acids
Res. 29:2994-3005.
Database: ../../../../database/env_nr
6,964,945 sequences; 1,385,475,744 total letters
The options "-gpu_blocks" and "-gpu_threads" are optional when creating the GPU
database. If they are not specified, their default values are 512 and 64, respectively.
NOTE: the option "-method" is incompatible with "-num_threads".
This will create the files "sorted_env_nr.gpu" and "sorted_env_nr.gpuinfo" in the same
directory with "sorted_env_nr".
Step 3. Executing GPU-BLAST
You are now ready to use GPU-BLAST. To search the database with the query
"SequenceLength_00000100.txt", type
[ploskas@anaximander bin]$ ./blastp -query ../../../../queries/SequenceLength_00000100.txt -db ../../../../database/sorted_env_nr -gpu t
BLASTP 2.2.28+
Reference: Stephen F. Altschul, Thomas L. Madden, Alejandro A.
Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J.
Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of
protein database search programs", Nucleic Acids Res. 25:3389-3402.
Reference for composition-based statistics: Alejandro A. Schaffer,
L. Aravind, Thomas L. Madden, Sergei Shavirin, John L. Spouge, Yuri
I. Wolf, Eugene V. Koonin, and Stephen F. Altschul (2001),
"Improving the accuracy of PSI-BLAST protein database searches with
composition-based statistics and other refinements", Nucleic Acids
Res. 29:2994-3005.
Database: ../../../../database/env_nr
6,964,945 sequences; 1,385,475,744 total letters
Query= sp|Q91G65|032R_IIV6 Uncharacterized protein 032R OS=Invertebrate
iridescent virus 6 GN=IIV6-032R PE=4 SV=1
Length=100
Score E
Sequences producing significant alignments: (Bits) Value
ECC82777.1 hypothetical protein GOS_5867893, partial [marine me... 61.6 6e-11
GAH00199.1 unnamed protein product [marine sediment metagenome] 48.5 3e-06
EBG35402.1 hypothetical protein GOS_9447047 [marine metagenome] 47.4 5e-06
OIR15560.1 hypothetical protein GALL_38830 [mine drainage metag... 40.4 0.003
GAF70722.1 unnamed protein product [marine sediment metagenome] 38.9 0.014
EDE03225.1 hypothetical protein GOS_1201654 [marine metagenome] 38.1 0.021
ECN02724.1 hypothetical protein GOS_4064323, partial [marine me... 38.1 0.026
KKK92759.1 hypothetical protein LCGC14_2699710, partial [marine... 36.6 0.088
OIR08757.1 hypothetical protein GALL_91410 [mine drainage metag... 35.0 0.25
KKK91461.1 hypothetical protein LCGC14_2712760 [marine sediment... 33.9 0.77
EBJ79500.1 hypothetical protein GOS_8838565, partial [marine me... 32.0 4.3
ECT65541.1 hypothetical protein GOS_5098259, partial [marine me... 31.6 5.0
EBB41044.1 hypothetical protein GOS_238181 [marine metagenome] 31.6 5.3
EBB29372.1 hypothetical protein GOS_257812, partial [marine met... 31.2 7.6
KKM82403.1 hypothetical protein LCGC14_1319930 [marine sediment... 31.2 8.0
EBE52939.1 hypothetical protein GOS_9748365, partial [marine me... 31.2 8.0
CBI09278.1 conserved hypothetical protein [mine drainage metage... 31.2 8.5
EBQ63088.1 hypothetical protein GOS_7721906, partial [marine me... 31.2 9.5
EDI73951.1 hypothetical protein GOS_382468, partial [marine met... 31.2 9.5
EDG96131.1 hypothetical protein GOS_690898, partial [marine met... 31.2 9.6
EBV21546.1 hypothetical protein GOS_6939265, partial [marine me... 30.8 9.7
> ECC82777.1 hypothetical protein GOS_5867893, partial [marine
metagenome]
Length=137
Score = 61.6 bits (148), Expect = 6e-11, Method: Compositional matrix adjust.
Identities = 32/90 (36%), Positives = 53/90 (59%), Gaps = 1/90 (1%)
Query 10 KKKEVGQVAVLQ-KERLIFYIVTKEKSYLKPTLANFSNAIDSLYNECLLRKCCKLAIPKI 68
++ VGQ+A+L+ ++IFY+VTK K Y KP L + ++ L + ++A+PKI
Sbjct 46 QRAGVGQIAILKCHGQIIFYLVTKSKYYEKPNLWSIHASLLQLRRYMVDHCLTQIAMPKI 105
Query 69 GCCLDRLYWKTVKNIIIDKLCKKGIEVVVY 98
GC LDR+ W+ V+N++ I V +Y
Sbjct 106 GCGLDRMAWEDVENLLWSVFDNHNILVTIY 135
> GAH00199.1 unnamed protein product [marine sediment metagenome]
Length=156
Score = 48.5 bits (114), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 22/92 (24%), Positives = 52/92 (57%), Gaps = 1/92 (1%)
Query 10 KKKEVGQVAVLQKERL-IFYIVTKEKSYLKPTLANFSNAIDSLYNECLLRKCCKLAIPKI 68
+ ++G L+++ + IFY+VTK+ + KPT + +++++ + + + +++P+I
Sbjct 65 QPHQIGDTPYLERDGIVIFYLVTKKLYHQKPTYDSIEKSLETMRDIMIQKHIHDISMPRI 124
Query 69 GCCLDRLYWKTVKNIIIDKLCKKGIEVVVYYI 100
GC LD+ W ++ I+ I++ VY +
Sbjct 125 GCGLDKKNWTEIEKILGRVFKDTDIKISVYSL 156
> EBG35402.1 hypothetical protein GOS_9447047 [marine metagenome]
Length=140
Score = 47.4 bits (111), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 39/72 (54%), Gaps = 0/72 (0%)
Query 26 IFYIVTKEKSYLKPTLANFSNAIDSLYNECLLRKCCKLAIPKIGCCLDRLYWKTVKNIII 85
++ ++TK+K KPT ++ + N L ++A+PKIGC LD+L W V+ II
Sbjct 66 VYNLITKKKYSGKPTYQTIRMSLVIMRNHALANNITRIAMPKIGCGLDKLQWAMVRAIIH 125
Query 86 DKLCKKGIEVVV 97
+ IE+ V
Sbjct 126 ELFEDTDIEIRV 137
> OIR15560.1 hypothetical protein GALL_38830 [mine drainage metagenome]
Length=163
Score = 40.4 bits (93), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 28/102 (27%), Positives = 48/102 (47%), Gaps = 8/102 (8%)
Query 5 KFCYNKKKEVGQVAVLQKE--RLIFYIVTKEKSYL---KP---TLANFSNAIDSLYNECL 56
+C + + G++ R + + T++ +Y KP TL + ++++ +L N
Sbjct 48 HYCQTQHPKSGELWTWMSADGRYLVNLFTQDAAYAHGSKPGNATLHHINHSLHALRNFVQ 107
Query 57 LRKCCKLAIPKIGCCLDRLYWKTVKNIIIDKLCKKGIEVVVY 98
K LA+P++ C + L W VK II L GI V VY
Sbjct 108 KEKVGSLALPRLACGVGGLNWDDVKLIIEKHLGDLGIPVYVY 149
> GAF70722.1 unnamed protein product [marine sediment metagenome]
Length=199
Score = 38.9 bits (89), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 28/100 (28%), Positives = 45/100 (45%), Gaps = 6/100 (6%)
Query 5 KFCYNKKKEVG-----QVAVLQKERLIFYIVTKEKSYLKPTLANFSNAIDSLYNECLLRK 59
K C +KK G Q+ +L + + I TK K L + +++L E
Sbjct 48 KVCKDKKLHPGMVYTYQLLILGRTQYIINFPTKRHWKGKSKLEDIQQGLEALAQEIKRLG 107
Query 60 CCKLAIPKIGCCLDRLYWKTVKNIIIDKLCK-KGIEVVVY 98
++IP +GC L L W+TV+ I+ L +EV +Y
Sbjct 108 IRSISIPPLGCGLGGLNWETVRPIMESALVSLTDVEVDIY 147
> EDE03225.1 hypothetical protein GOS_1201654 [marine metagenome]
Length=158
Score = 38.1 bits (87), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 21/79 (27%), Positives = 39/79 (49%), Gaps = 0/79 (0%)
Query 20 LQKERLIFYIVTKEKSYLKPTLANFSNAIDSLYNECLLRKCCKLAIPKIGCCLDRLYWKT 79
++ E IF + T++ K TL + ++ S+ + + IP+IG L L W
Sbjct 66 VEGENTIFNLGTQKTWRTKATLDAVATSLGSMLAIAQAKGIKCIGIPRIGAGLGGLVWDD 125
Query 80 VKNIIIDKLCKKGIEVVVY 98
VK II ++ K + ++V+
Sbjct 126 VKAIIQEEAQKSDVTLIVF 144
> ECN02724.1 hypothetical protein GOS_4064323, partial [marine
metagenome]
Length=206
Score = 38.1 bits (87), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 33/64 (52%), Gaps = 8/64 (13%)
Query 43 NFSNAIDSLYNECLLRKCCKLAIPKIGCCLDRLYW-------KTVKNIIIDKLCKKGIEV 95
N N+ D YN L+ K + IPK+G D +Y + ++N +++KL KGI
Sbjct 86 NRKNSAD-FYNHLLVEKIHDVGIPKVGDNRDHVYQMYTITVEEKIRNEVVEKLNSKGIGA 144
Query 96 VVYY 99
V++
Sbjct 145 SVHF 148
> KKK92759.1 hypothetical protein LCGC14_2699710, partial [marine
sediment metagenome]
Length=226
Score = 36.6 bits (83), Expect = 0.088, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 30/65 (46%), Gaps = 0/65 (0%)
Query 20 LQKERLIFYIVTKEKSYLKPTLANFSNAIDSLYNECLLRKCCKLAIPKIGCCLDRLYWKT 79
LQ R + TK K + + + ++SL E R +AIP +GC L L W
Sbjct 68 LQLPRYVINFPTKRHWKGKSRIEDIESGLNSLITEVRQRNIESIAIPPLGCGLGGLDWGV 127
Query 80 VKNII 84
V+ ++
Sbjct 128 VRPMV 132
> OIR08757.1 hypothetical protein GALL_91410 [mine drainage metagenome]
Length=162
Score = 35.0 bits (79), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 23/102 (23%), Positives = 48/102 (47%), Gaps = 8/102 (8%)
Query 5 KFCYNKKKEVGQVAVLQKE--RLIFYIVTKEKSY---LKP---TLANFSNAIDSLYNECL 56
+C + + G++ R + + T++ +Y KP TL++ ++ + +L +
Sbjct 48 HYCQTQHPKPGELWTWMSADGRYLVNLFTQDGAYDHGSKPGHATLSHVNHTLHALRSFAQ 107
Query 57 LRKCCKLAIPKIGCCLDRLYWKTVKNIIIDKLCKKGIEVVVY 98
K LA+P++ C ++ L W VK +I L I + +Y
Sbjct 108 KEKVPSLALPRLSCGINGLDWNDVKPLIEKHLGDLNIPIYIY 149
> KKK91461.1 hypothetical protein LCGC14_2712760 [marine sediment
metagenome]
Length=150
Score = 33.9 bits (76), Expect = 0.77, Method: Compositional matrix adjust.
Identities = 22/82 (27%), Positives = 38/82 (46%), Gaps = 1/82 (1%)
Query 17 VAVLQKERLIFYIVTKEKSYLKPTLANFSNAIDSLYNECLLRKCCKLAIPKIGCCLDRLY 76
V + RL+ + V K + + L ++ + L C K K+A+P+ GC RL
Sbjct 65 VHTFGQYRLMTFPV-KYHWHEEADLDLIRHSCEQLRGLCYTLKMAKVAMPRPGCGNGRLD 123
Query 77 WKTVKNIIIDKLCKKGIEVVVY 98
W V+ ++ + L E +VY
Sbjct 124 WDDVRPVLEETLGDSRTEFLVY 145
> EBJ79500.1 hypothetical protein GOS_8838565, partial [marine
metagenome]
Length=419
Score = 32.0 bits (71), Expect = 4.3, Method: Composition-based stats.
Identities = 18/67 (27%), Positives = 34/67 (51%), Gaps = 0/67 (0%)
Query 16 QVAVLQKERLIFYIVTKEKSYLKPTLANFSNAIDSLYNECLLRKCCKLAIPKIGCCLDRL 75
QVA+ + +F V KE++Y LA+ SNA+ ++ + ++ C K + +
Sbjct 198 QVAIALENAQLFEEVAKERTYSDSMLASMSNAVVTINEDGIIATCNKAGLKIFRVSAQEI 257
Query 76 YWKTVKN 82
KTV++
Sbjct 258 IGKTVED 264
> ECT65541.1 hypothetical protein GOS_5098259, partial [marine
metagenome]
Length=145
Score = 31.6 bits (70), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 15/47 (32%), Positives = 27/47 (57%), Gaps = 0/47 (0%)
Query 16 QVAVLQKERLIFYIVTKEKSYLKPTLANFSNAIDSLYNECLLRKCCK 62
QVA+ + +F V KE++Y LA+ SNA+ ++ + ++ C K
Sbjct 99 QVAIALENAQLFEEVAKERTYSDSMLASMSNAVVTINEDGIIATCNK 145
> EBB41044.1 hypothetical protein GOS_238181 [marine metagenome]
Length=215
Score = 31.6 bits (70), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 15/47 (32%), Positives = 23/47 (49%), Gaps = 0/47 (0%)
Query 54 ECLLRKCCKLAIPKIGCCLDRLYWKTVKNIIIDKLCKKGIEVVVYYI 100
E + + +P + L R+ WKT ++IDKL GI + YI
Sbjct 136 EYGFKNLSDIHVPNLFKNLSRVMWKTYDELLIDKLIVNGIANKIQYI 182
> EBB29372.1 hypothetical protein GOS_257812, partial [marine metagenome]
Length=166
Score = 31.2 bits (69), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 20/77 (26%), Positives = 38/77 (49%), Gaps = 1/77 (1%)
Query 25 LIFYIVTKEKSYLKPTLANFSNAIDS-LYNECLLRKCCKLAIPKIGCCLDRLYWKTVKNI 83
L+ Y + ++ Y+ + S+ I S L +E + + +P + L R+ WKT +
Sbjct 57 LLSYFIYYKRQYIDINIFKRSSRIYSILSSEYGFKNLSDIHVPNLFKNLSRVMWKTYDEL 116
Query 84 IIDKLCKKGIEVVVYYI 100
IDKL GI ++++
Sbjct 117 FIDKLIVNGIANKIHHV 133
> KKM82403.1 hypothetical protein LCGC14_1319930 [marine sediment
metagenome]
Length=345
Score = 31.2 bits (69), Expect = 8.0, Method: Composition-based stats.
Identities = 28/105 (27%), Positives = 48/105 (46%), Gaps = 10/105 (10%)
Query 4 YK-FCYNKKKEVGQVAVLQKERLI-----FYIV---TKEKSYLKPTLANFSNAIDSLYNE 54
YK C + + GQ+ V + L Y+V TK K ++ + +D+L +
Sbjct 47 YKSLCDGNELQPGQMFVFDTKSLFEAEGPRYLVNFPTKAHWRSKSKISYVEDGLDALVST 106
Query 55 CLLRKCCKLAIPKIGCCLDRLYWKTVKNIIIDKLCK-KGIEVVVY 98
+ IP +GC L W VK +I+ KL +G+++VV+
Sbjct 107 IREYGIKSIGIPPLGCGNGGLDWAQVKPLIVSKLSGLEGVDIVVF 151
> EBE52939.1 hypothetical protein GOS_9748365, partial [marine
metagenome]
Length=492
Score = 31.2 bits (69), Expect = 8.0, Method: Composition-based stats.
Identities = 19/67 (28%), Positives = 33/67 (49%), Gaps = 0/67 (0%)
Query 16 QVAVLQKERLIFYIVTKEKSYLKPTLANFSNAIDSLYNECLLRKCCKLAIPKIGCCLDRL 75
QVA+ + +F V KE++Y LA+ SNA+ ++ E + C K + +
Sbjct 55 QVAIALENAQLFEEVAKERTYSDSMLASMSNAVVTINEEGKIATCNKAGLKIFRVGTQEI 114
Query 76 YWKTVKN 82
KTV++
Sbjct 115 VGKTVED 121
> CBI09278.1 conserved hypothetical protein [mine drainage metagenome]
Length=368
Score = 31.2 bits (69), Expect = 8.5, Method: Composition-based stats.
Identities = 16/36 (44%), Positives = 19/36 (53%), Gaps = 0/36 (0%)
Query 63 LAIPKIGCCLDRLYWKTVKNIIIDKLCKKGIEVVVY 98
LAIP +GC L W V I+ KL GI V +Y
Sbjct 108 LAIPPLGCGNGGLEWTLVGPIMYQKLASLGISVDIY 143
> EBQ63088.1 hypothetical protein GOS_7721906, partial [marine
metagenome]
Length=475
Score = 31.2 bits (69), Expect = 9.5, Method: Composition-based stats.
Identities = 19/67 (28%), Positives = 33/67 (49%), Gaps = 0/67 (0%)
Query 16 QVAVLQKERLIFYIVTKEKSYLKPTLANFSNAIDSLYNECLLRKCCKLAIPKIGCCLDRL 75
QVA+ + +F V KE++Y LA+ SNA+ ++ E + C K + +
Sbjct 112 QVAIALENAQLFEEVAKERTYNDSMLASMSNAVVTINEEGKIATCNKAGLKIFRVSTPEI 171
Query 76 YWKTVKN 82
KTV++
Sbjct 172 VGKTVED 178
> EDI73951.1 hypothetical protein GOS_382468, partial [marine metagenome]
Length=601
Score = 31.2 bits (69), Expect = 9.5, Method: Composition-based stats.
Identities = 19/67 (28%), Positives = 33/67 (49%), Gaps = 0/67 (0%)
Query 16 QVAVLQKERLIFYIVTKEKSYLKPTLANFSNAIDSLYNECLLRKCCKLAIPKIGCCLDRL 75
QVA+ + +F V KE++Y LA+ SNA+ ++ E + C K + +
Sbjct 349 QVAIALENAQLFEEVAKERTYSDSMLASMSNAVVTINEERKIATCNKAGLKIFRVSTPEI 408
Query 76 YWKTVKN 82
KTV++
Sbjct 409 VGKTVED 415
> EDG96131.1 hypothetical protein GOS_690898, partial [marine metagenome]
Length=696
Score = 31.2 bits (69), Expect = 9.6, Method: Composition-based stats.
Identities = 17/67 (25%), Positives = 34/67 (51%), Gaps = 0/67 (0%)
Query 16 QVAVLQKERLIFYIVTKEKSYLKPTLANFSNAIDSLYNECLLRKCCKLAIPKIGCCLDRL 75
QVA+ + +F V +E++Y LA+ SNA+ ++ + ++ C K + +
Sbjct 376 QVAIALENAQLFEEVARERTYSDSMLASMSNAVVTINEDGIIATCNKAGLKIFRVSAQEI 435
Query 76 YWKTVKN 82
KTV++
Sbjct 436 VGKTVED 442
> EBV21546.1 hypothetical protein GOS_6939265, partial [marine
metagenome]
Length=282
Score = 30.8 bits (68), Expect = 9.7, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 31/60 (52%), Gaps = 4/60 (7%)
Query 3 VYKFCYNKKKEVGQVAVLQKERLIFYIVTKEKSYLKPTLANFSNAIDSLYNECLLRKCCK 62
+YK+ +N K E+G+ A+ T +KS+LK + + N D ++E L+R +
Sbjct 57 MYKYIFNPKTELGEKAITSWSEY----YTTDKSFLKDSQKVYKNMKDFPFDESLIRNMLE 112
Lambda K H a alpha
0.327 0.143 0.446 0.792 4.96
Gapped
Lambda K H a alpha sigma
0.267 0.0410 0.140 1.90 42.6 43.6
Effective search space used: 33829893504
Database: ../../../../database/env_nr
Posted date: Mar 4, 2017 6:26 PM
Number of letters in database: 1,385,475,744
Number of sequences in database: 6,964,945
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Neighboring words threshold: 11
Window for multiple hits: 40
NOTE: if during execution you get the message
WARNING: Not enough GPU global memory to process volume No. 00 of the database. Continuing without the GPU...
Consider splitting the input database in volumes with smaller size by using the option "-max_file_size <String>" (e.g. -max_file_sz 500MB).
Consider using fewer GPU blocks and then fewer GPU thread when formatting the database with (e.g. "-gpu_blocks 256" and/or "-gpu_threads 32") to reduce the GPU global memory requirements.
then your GPU does not have enough global memory to carry out the sequence alignment of the
current database volume under the current GPU database configuration. To overcome this problem, you
can reformat the database with "makeblastdb" with a value for "-max_file_sz" smaller than your
previous choice. Another option is to recreate the GPU database by using the options "-method 2" and
smaller values for "-gpu_blocks" and/or "-gpu_threads" than your previous choices (or use smaller
values than 512 and 64 if you let GPU-BLAST create the GPU database with the default values as shown
in the example above).
Timing the execution time
[ploskas@anaximander bin]$ time ./blastp -query ../../../../queries/SequenceLength_00000100.txt -db ../../../../database/sorted_env_nr -gpu t > gpu_output.txt
real 0m5.614s
user 0m4.072s
sys 0m1.543s
[ploskas@anaximander bin]$ time ./blastp -query ../../../../queries/SequenceLength_00000100.txt -db ../../../../database/sorted_env_nr -gpu f > cpu_output.txt
real 0m11.125s
user 0m10.937s
sys 0m0.196s
[ploskas@anaximander bin]$ diff cpu_output.txt gpu_output.txt