Difference between revisions of "MPIBLAST"

Revision as of 17:58, 6 June 2012

GETTING STARTED

Mpiblast is not loaded by default on the clusters therefore load the module before submitting any jobs:

module load mpiblast/1.6.0

EXAMPLE1 - DROSOPH

Copy sample problem files (fasta database and input) into a directory under work:

mkdir -p /work/$USER/samples/mpiblast/test1; rm /work/$USER/samples/mpiblast/test1/*; cd /work/$USER/samples/mpiblast/test1
cp /opt/sharcnet/mpiblast/1.6.0/examples/drosoph.in drosoph.in
gunzip -c /opt/sharcnet/mpiblast/1.6.0/examples/drosoph.nt.gz > drosoph.nt

Create hidden configuration file to define a Shared storage location between nodes and a Local storage directory available on each compute node where $USER should be replaced with your username as shown here:

[username@orc-login1:/work/roberpj/samples/mpiblast/test1] vi .ncbirc

[BLAST]
BLASTDB=/scratch/$USER/mpiblasttest1
BLASTMAT=/work/$USER/samples/mpiblast/test1
[mpiBLAST]
Shared=/scratch/$USER/mpiblasttest1
Local=/tmp

Partition the database into 8 fragments to a cluster local scratch storage location:

mkdir /scratch/$USER/mpiblasttest1; rm -f /scratch/$USER/mpiblasttest1/*; cd /work/$USER/samples/mpiblast/test1
mpiformatdb -N 8 -i drosoph.nt -o T -p F -n /scratch/$USER/testmpiblast1

Submit a short job with a 15m time limit on 8 plus 2 cores. If all goes well output results will be written to drosoph.out and the execution time will appear in ofile%J where %J is the job number:

cd /work/$USER/samples/mpiblast/test1
sqsub -r 15m -n 10 -q mpi -o ofile%J mpiblast -d drosoph.nt -i drosoph.in -p blastn -o drosoph.out --use-parallel-write --use-virtual-frags

Sample output results computed previously with BLASTN 2.2.15 [Oct-15-2006] are included in /opt/sharcnet/mpiblast/1.6.0/examples/ROSOPH.out to compare your newly generated drosoph.out file with.

EXAMPLE2 - BIOBREW

This example is provided to show some extra options and switchs that maybe useful for debugging and dealing with larger databases. As before copy sample problem files into a directory under work:

mkdir /work/$USER/samples/mpiblast/test2; rm /work/$USER/samples/mpiblast/test2/*; cd /work/$USER/samples/mpiblast/test2
cp /opt/sharcnet/mpiblast/1.6.0/examples/il2ra.in il2ra.in
gunzip -c /opt/sharcnet/mpiblast/1.6.0/examples/Hs.seq.uniq.gz > Hs.seq.uniq

Create hidden configuration file using the vi editor to define a Shared storage location between nodes and a Local storage directory available on each compute node as follows, where the Data directory is not yet populated or used in this example and hence can be omitted, where $USER should be replaced with your username as shown here:. If its desired the Local and Shared directories are the same then replace --copy-via=mpi with --copy-via=none as will be demonstrated in the below sqsub commands.

[username@orc-login1:/work/roberpj/samples/mpiblast/test1] vi .ncbirc

[NCBI]
Data=/opt/sharcnet/mpiblast/1.6.0/data
[BLAST]
BLASTDB=/work/$USER/mpiblasttest2
BLASTMAT=/work/$USER/samples/mpiblast/test2
[mpiBLAST]
Shared=/work/$USER/mpiblasttest2
Local=/tmp

Partition the database into 16 fragments directly in the work directly:

mkdir -p /scratch/$USER/mpiblasttest2; rm -f /scratch/$USER/mpiblasttest2/*; cd /work/$USER/samples/mpiblast/test1
mpiformatdb -N 16 -i Hs.seq.uniq -o T -p F                                          

Submit a couple of short jobs 15m time limit. If all goes well output results will be written to biobrewA.out and biobrewB.out and the execution time will appear in corresponding ofile%J's where %J is the job number.

A) In this job submission fragment files are first copied from work to local /tmp before being used (appropriate if work is slow). Usage of the profile option is also shown in this example:

cd /work/$USER/samples/mpiblast/test2; rm -f oTime*
sqsub -r 15m -n 18 -q mpi -o ofile%J mpiblast  --use-parallel-write --copy-via=mpi -d Hs.seq.uniq -i il2ra.in -p blastn -o biobrew.out --time-profile=oTime

B) In this job submission fragment files are used inplace on work. Usage of the debug option is also shown in this example.

cd /work/$USER/samples/mpiblast/test2; rm -f oLog*
sqsub -r 15m -n 18 -q mpi -o ofile%J mpiblast --use-parallel-write --copy-via=none -d Hs.seq.uniq -i il2ra.in -p blastn -o biobrew.out --debug=oLog

Finally compare /opt/sharcnet/mpiblast/1.6.0/examples/BIOBREW.out computed previously with BLASTN 2.2.15 [Oct-15-2006] with your newly generated biobrew.out output file to verify the results and submit a ticket if there are any problems!

MPIBLAST BINARIES (command line arguments)

[roberpj@orc-login1:/opt/sharcnet/mpiblast/1.6.0/bin] ./mpiblast -help
mpiBLAST requires the following options: -d [database] -i [query file] -p [blast program name]

[roberpj@orc-login1:/opt/sharcnet/mpiblast/1.6.0/bin] ./mpiformatdb --help
Executing: formatdb - 

formatdb 2.2.20   arguments:

  -t  Title for database file [String]  Optional
  -i  Input file(s) for formatting [File In]  Optional
  -l  Logfile name: [File Out]  Optional
    default = formatdb.log
  -p  Type of file
         T - protein   
         F - nucleotide [T/F]  Optional
    default = T
  -o  Parse options
         T - True: Parse SeqId and create indexes.
         F - False: Do not parse SeqId. Do not create indexes.
 [T/F]  Optional
    default = F
  -a  Input file is database in ASN.1 format (otherwise FASTA is expected)
         T - True, 
         F - False.
 [T/F]  Optional
    default = F
  -b  ASN.1 database in binary mode
         T - binary, 
         F - text mode.
 [T/F]  Optional
    default = F
  -e  Input is a Seq-entry [T/F]  Optional
    default = F
  -n  Base name for BLAST files [String]  Optional
  -v  Database volume size in millions of letters [Integer]  Optional
    default = 4000
  -s  Create indexes limited only to accessions - sparse [T/F]  Optional
    default = F
  -V  Verbose: check for non-unique string ids in the database [T/F]  Optional
    default = F
  -L  Create an alias file with this name
        use the gifile arg (below) if set to calculate db size
        use the BLAST db specified with -i (above) [File Out]  Optional
  -F  Gifile (file containing list of gi's) [File In]  Optional
  -B  Binary Gifile produced from the Gifile specified above [File Out]  Optional
  -T  Taxid file to set the taxonomy ids in ASN.1 deflines [File In]  Optional
  -N  Number of database volumes [Integer]  Optional
    default = 0