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Blast on Biowulf

BLAST on Biowulf is intended for running a large number of sequence files, such as hundreds or thousands of query sequences, against the Blast databases. If you have just a few query sequences, you should use Blast on the NCBI website or on Helix. All NCBI Blast programs - blastn, blastp, blastx, tblastn, tblastx, blastpgp, megablast,rpsblast -- are available on Biowulf. Please contact the Helix Systems staff, or 4-6248) if you have questions about your Blast jobs.

Version: The output from every Blast program includes the version number.

The 'easyblast' program on Biowulf simplifies submission of large Blast jobs. You need to put all your query sequences into a directory, and then type 'easyblast' at the Biowulf prompt. You will be prompted for all required parameters. The script will then decide what kind of nodes you need (based on the database you are BLASTing against), and submit your job to as many nodes as are available (max 32). Sample session (user input is in bold):
biowulf% easyblast

EasyBlast: Blast for large numbers of sequences
Enter the directory which contains your input sequences: /data/username/blast/seqs

Enter the directory where you want your Blast output to go: /data/username/blast/out
** WARNING: There are already files in /data/username/blast/out which will be 
overwritten by this job.
** Continue? (y/n) :y

BLAST programs:
    blastn - nucleotide query sequence against nucleotide database
    blastp - protein query sequence against protein database
    blastx - nucleotide query translated in all 6 reading frames
                      against a protein database
    tblastn - protein query sequence against a nucleotide database
                      translated in all 6 reading frames
    tblastx - 6-frame translations of a nucleotide query sequence
                      against the 6-frame translations of a nucleotide database
    blastpgp - PSI-BLAST protein query against protein database
    megablast - EST-type query sequences against nucleotide database
Which program do you want to run: blastn

The following nucleotide databases are available:(
(or enter your own database with full pathname)
    nt - NCBI nonredundant Genbank+EMBL+DDBJ+PDB (no EST, STS, GSS or HTG)
    est_human - nonredundant Genbank+EMBL+DDBJ EST human sequences
    est_mouse - nonredundant Genbank+EMBL+DDBJ EST mouse sequences
    est_others - nonredundant Genbank+EMBL+DDBJ EST all other organisms
    pdbnt - from the 3-dimensional structures 
    htgs - high throughput genome sequences
    ecoli.nt - ecoli genomic sequences
    mito.nt - mitochondrial sequences
    yeast.nt - yeast (Saccharomyces cerevisiae) genomic sequences
    drosoph.nt - drosophila sequences
    hs_genome - human genome assembly (Build 36, Apr 2006)
    hs_genome.rna - human genome RNA (Build 36, Apr 2006)
    mouse_genome - mouse genome assembly (Build 36, Mar 2006)
    mouse_genome.rna - mouse genome RNA (Build 36, Mar 2006)
    mouse_masked - mouse genome, masked (Build 36, Mar 2006)
    other_genomic - non-human genomic sequences
    human.rna - RefSeq human RNA
    mouse.rna - RefSeq mouse RNA

Database to run against: yeast

Want a summary file in the output directory? (y/n, default y) : has a full list of 
available parameters. Any additional Blast parameters (e.g. -v 10): Submitting to 8 nodes with :g4 memory. Job number is 85633.biobos Monitor your job at

easyblast figures out the node memory required, sets up all temporary files and directories, and submits the job for you.

If a summary has been requested, a file called 'summary' will appear in your output directory along with the actual Blast outputs. For your convenience, this will contain the hits from each Blast result so you can scroll through it easily. Sample summary file.

To run against your own database, enter the db name with full path at the Database: prompt. For example:

       Database to run against: /data/username/blast_db/my_db
Database files have suffixes like .nsq, .nin (nucleotide), .psq, .psi (protein) etc. You should enter the full path and the database name without the suffix.

You can put multiple sequences into each of your input sequence files. However, there needs to be at least as many query sequence files as nodes! Very occasionally Blast may barf on a particular sequence, in which case it will not continue on to other sequences in that file. If your query sequences are all in one file, and you need to split them into multiple sequence files, there are a couple of utilities available: Some recent runs on our system to give you an idea of what sort of performance to expect.
Query Database Blast program
v 2.2.13
Nodes Time
1000 nucleotide
EST sequences
updated 4/Dec/2008
7,808,957 sequences
6.2 GB
blastn 16 nodes
2.6 GHz dual-core Opterons
Gb ethernet
21 mins
updated 4/Dec/2008
7,463,447 sequences
2.4 GB
blastx 16 nodes
2.6 GHz dual-core Opterons
Gb ethernet
21 mins
updated 4/Dec/2008
8,163,883 sequences
1.1 GB
blastn 16 nodes
2.6 GHz dual-core Opterons
Gb ethernet
5.5 mins
human genome
updated Apr 2006
25 sequences
770 Mb
blastn 16 nodes
2.6 GHz dual-core Opterons
Gb ethernet
40 mins

1000 protein sequences nr
updated 15/Dec/2008
7,463,447 sequences
2.4 GB
blastp 16 nodes
2.6 GHz dual-core Opterons
Gb ethernet
28 mins
updated 4/Dec/2008
7,808,957 sequences
6.2 GB
tblastn 16 nodes
2.6 GHz dual-core Opterons
Gb ethernet
3:47 hrs

BLAST Databases
Local copies of the sequence databases used by blast can be found in the directory /fdb/blastdb. These data are a (weekly-updated) mirror of the directory maintained by NCBI. Some dbs were built from Fasta-format files, with the command:

formatdb -o T

Running via swarm

Easyblast uses swarm. If you prefer to use swarm directly, set up a swarm command file along the following lines. You have several options for setting up the environment:

  1. use '--module blast/2.2.26' in your swarm command
  2. OR Use the full path for blastall: /usr/local/blast/ncbi/bin/blastall
  3. OR Use 'module load blast' in each line in the swarm command file, as in the example below.
  4. OR add /usr/local/blast/ncbi/bin to your PATH in your .bashrc or .cshrc file
# this file is called blastcmd
blastall -a 4 -p blastn -d /fdb/blastdb/nt -i /data/user/myseqs/seq1.fas -o /data/user/blastout/seq1.out
blastall -a 4 -p blastn -d /fdb/blastdb/nt -i /data/user/myseqs/seq2.fas -o /data/user/blastout/seq2.out
blastall -a 4 -p blastn -d /fdb/blastdb/nt -i /data/user/myseqs/seq3.fas -o /data/user/blastout/seq3.out
blastall -a 4 -p blastn -d /fdb/blastdb/nt -i /data/user/myseqs/seq4.fas -o /data/user/blastout/seq4.out

Determine the size of the database file (see the section on Blast and node memory). Let's assume the database is 8.3 GB. Round upwards to 9 GB. Swarm will be told that each command requires 9 GB with the '-g 9' flag.
The '-a 4' flag to the blastall commands above tell blastall to run with 4 threads. Therefore, swarm has to be told that each command above will require 4 cores, with the '-t 4' flag. Submit this swarm with

swarm -g 9 -t 4 -f blastcmd --module blast/2.2.26
Note that the Blast + versions (e.g. Blast 2.2.27+) do not include a 'blastall' executable. [Brief summary of differences between '+' and legacy versions]

Blast Database Update Status -- status of all Blast databases installed on the system.

When analyzing a large number of sequences with blast it is imperative that the blast database fit entirely within the memory of a given node... this makes a vast difference in the performance of blast. Thus, if you are running Blast via swarm, you need to check the size of the database.
biowulf% ls -lh my_db.nsq
-rw-rw-r--   1 username  username     1.5G Aug 31  2011 my_db.nsq
The database is 1.5 GB, so you would submit to swarm with '-g 2' (2 GB required for each Blast run).

For multi-part databases such as 'human_genomic', you need to add the size of al the sections. e.g.

[user@biowulf ~]# ls -l /fdb/blastdb/human_genomic*.nsq
-rw-rw-r-- 1 helixapp staff 945M  Oct  1 22:11 /fdb/blastdb/human_genomic.00.nsq
-rw-rw-r-- 1 helixapp staff 957M  Oct  1 22:12 /fdb/blastdb/human_genomic.01.nsq
-rw-rw-r-- 1 helixapp staff 274M  Oct  1 22:12 /fdb/blastdb/human_genomic.02.nsq
The total database size for the human_genomic database is thus ~1GB + ~1GB + .27 GB = 2.3 GB. You would submit to swarm with '-g 3' (3 GB required for each Blast run)

If you are using Easyblast, the Easyblast script will determine the database size and submit the job to the appropriate nodes.

Scanning through a large set of Blast results can be time-consuming. The blast_summary script may help. Go to your blast output directory and type:

and it will create a file in that directory called 'summary' which contains just the Blast hits for each query sequence. Easyblast does this automatically for you.

These are the parameters available for the blastall program. See also (the Blast documentation at the NCBI website)
blastall 2.2.17 arguments:

  -p  Program Name [String]
  -d  Database [String]
    default = nr
  -i  Query File [File In]
    default = stdin
  -e  Expectation value (E) [Real]
    default = 10.0
  -m  alignment view options:
0 = pairwise,
1 = query-anchored showing identities,
2 = query-anchored no identities,
3 = flat query-anchored, show identities,
4 = flat query-anchored, no identities,
5 = query-anchored no identities and blunt ends,
6 = flat query-anchored, no identities and blunt ends,
7 = XML Blast output,
8 = tabular, 
9 tabular with comment lines
10 ASN, text
11 ASN, binary [Integer]
    default = 0
    range from 0 to 11
  -o  BLAST report Output File [File Out]  Optional
      default = stdout
  -F  Filter query sequence (DUST with blastn, SEG with others) [String]
      default = T
  -G  Cost to open a gap (-1 invokes default behavior) [Integer]
      default = -1
  -E  Cost to extend a gap (-1 invokes default behavior) [Integer]
      default = -1
  -X  X dropoff value for gapped alignment (in bits) (zero invokes default
      behavior) blastn 30, megablast 20, tblastx 0, all others 15 [Integer]
      default = 0
  -I  Show GI's in deflines [T/F]
      default = F
  -q  Penalty for a nucleotide mismatch (blastn only) [Integer]
      default = -3
  -r  Reward for a nucleotide match (blastn only) [Integer]
      default = 1
  -v  Number of database sequences to show one-line descriptions for (V)
      default = 500
  -b  Number of database sequence to show alignments for (B) [Integer]
      default = 250
  -f  Threshold for extending hits, default if zero
      blastp 11, blastn 0, blastx 12, tblastn 13
      tblastx 13, megablast 0 [Real]
      default = 0
  -g  Perform gapped alignment (not available with tblastx) [T/F]
      default = T
  -Q  Query Genetic code to use [Integer]
      default = 1
  -D  DB Genetic code (for tblast[nx] only) [Integer]
      default = 1
  -a  Number of processors to use [Integer]
      default = 1
  -O  SeqAlign file [File Out]  Optional
  -J  Believe the query defline [T/F]
      default = F
  -M  Matrix [String]
      default = BLOSUM62
  -W  Word size, default if zero (blastn 11, megablast 28, all others 3)
      default = 0
  -z  Effective length of the database (use zero for the real size) [Real]
      default = 0
  -K  Number of best hits from a region to keep (off by default, if used a value
      of 100 is recommended) [Integer]
      default = 0
  -P  0 for multiple hit, 1 for single hit (does not apply to blastn) [Integer]
      default = 0
  -Y  Effective length of the search space (use zero for the real size) [Real]
      default = 0
  -S  Query strands to search against database (for blast[nx], and tblastx)
      3 is both, 1 is top, 2 is bottom [Integer]
      default = 3
  -T  Produce HTML output [T/F]
      default = F
  -l  Restrict search of database to list of GI's [String]  Optional
  -U  Use lower case filtering of FASTA sequence [T/F]  Optional
  -y  X dropoff value for ungapped extensions in bits (0.0 invokes default
      behavior) blastn 20, megablast 10, all others 7 [Real]
      default = 0.0
  -Z  X dropoff value for final gapped alignment in bits (0.0 invokes default
      behavior) blastn/megablast 50, tblastx 0, all others 25 [Integer]
      default = 0
  -R  PSI-TBLASTN checkpoint file [File In]  Optional
  -n  MegaBlast search [T/F]
      default = F
  -L  Location on query sequence [String]  Optional
  -A  Multiple Hits window size, default if zero (blastn/megablast 0, all others
      40 [Integer]
      default = 0
  -w  Frame shift penalty (OOF algorithm for blastx) [Integer]
      default = 0
  -t  Length of the largest intron allowed in a translated nucleotide sequence
      when linking multiple distinct alignments. (0 invokes default behavior; a
      negative value disables linking.) [Integer]
      default = 0
  -B  Number of concatenated queries, for blastn and tblastn [Integer]  Optional
      default = 0
  -V  Force use of the legacy BLAST engine [T/F]  Optional
      default = F
  -C  Use composition-based statistics for blastp or tblastn:
      As first character:
      D or d: default (equivalent to T)
      0 or F or f: no composition-based statistics
      1 or T or t: Composition-based statistics as in NAR 29:2994-3005, 2001
      2: Composition-based score adjustment as in Bioinformatics 21:902-911,
         2005, conditioned on sequence properties
      3: Composition-based score adjustment as in Bioinformatics 21:902-911,
         2005, unconditionally
      For programs other than tblastn, must either be absent or be D, F or 0.
      As second character, if first character is equivalent to 1, 2, or 3:
      U or u: unified p-value combining alignment p-value and compositional
      p-value in round 1 only [String]
      default = D
  -s  Compute locally optimal Smith-Waterman alignments (This option is only
      available for gapped tblastn.) [T/F]
      default = F