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Installed Sequence Analysis software

Phylogenetic/Linkage Analysis

Blast on Biowulf

Demo: How to run a large-scale Blast job on Biowulf
1. Transfer your sequence files to Biowulf.
   On a PC: use the ftp program (with all versions of Windows).
   On a Mac: use the Fetch program (downloadable from NIH Pubnet)
   On a Unix machine: use ftp (comes with all flavours of Unix).

   Open a connection to biowulf.nih.gov (or helix.nih.gov)
   Change directory to /data/username/
   Put your files into that directory.
   

2. Use EasyBlast to submit your jobs to the cluster. Sample session: (user input in bold)

   biobos% easyblast
   
   EasyBlast: Blast for large numbers of sequences
   Enter the directory which contains your input sequences: data/username/blast/myseqs
   
   Enter the directory where you want your Blast output to go: /data/username/blast/results
   ** WARNING: There are already files in /data/username/blast/results which will be deleted 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
   Which program do you want to run: blastn
   
   The following nucleotide databases are available:
   (or enter your own database with full pathname)
       nt - all nonredundant Genbank+EMBL+DDBJ+PDB (no EST, STS, GSS or HTG)
       hs_genome - human genome assembly (Build 33, 14 Apr 2003)
       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
       patnt - from the patent division of Genbank
       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.fna - RefSeq human sequences
       other_genomic - non-human genomic sequences
       mouse_genome - mouse genome
       mouse_masked - mouse genome, masked
   Database to run against: nt
   
    Want a summary file in the output directory? (y/n, default y) : n
   
   http://biowulf.nih.gov/apps/blast.htmlg has a full list of available parameters.
   Any additional Blast parameters (e.g. -v 10): 
   Checking node situation....
   
   Submitting to 20 nodes. Job number is 709061.biobos
   
   Monitor your job at http://biowulf.nih.gov/cgi-bin/queuemon?709061.biobos
   
   

Use the URL that EasyBlast gives you to watch your job run. You can see the full range of Biowulf monitors at http://biowulf.nih.gov/sysmon/

Blue: no load
Green: load ~ 1
Yellow: load ~ 2 (i.e. fully utilized)
Red: load > 2 (problem?)

What to expect:

Contact the helix staff (staff@helix.nih.gov or 4-6248) if you have questions or concerns about your job.

What EasyBlast does

1. Checks that your input sequences exist and that at least one file contains a Fasta sequence.
2. Checks if the output directory exists. Warns you if there are already files in that directory which may be over-written.
3. Lists the available Blast programs for you to choose.
4. Lists the appropriate (nucleotide or protein) databases for your choice.
5. Calculates the node memory required based on size of database. (i.e. 'type' of node).
6. Writes an environment file with the name of database, name of program, input and output directories, and other parameters that the actual Blast job will use.
7. Checks the current available node situation, and submits to as many nodes as possible (max 32).
8. Writes a summary file in the output directory containing just the 'hits' from each Blast output.

Note: To run against your own database, enter its full pathname. e.g.

Database to run against: /data/username/blast_db/my_own_db

Benchmarks

Blastn
Query: 1000 nucleotide EST sequences
Database: NCBI nt nucleotide database (1,431,631 sequences, 1.8 Gb)

Serial blast runs with GCG's Netblast against NCBI server ~ 18 hrs
Silicon Graphics R14000, 4 processors (nimbus.nih.gov) - 5.5 hrs
10 Biowulf p2800 nodes: 33 mins

Example 2: Repeatmasker

This program is NOT parallelized on Biowulf. The advantage of using the Biowulf cluster would be to run Repeatmasker on a large number of sequences.

1. Set up a command file with one line for each command.

   repeatmasker NM_00110*
   repeatmasker NM_00111*
   repeatmasker NM_00112*
   repeatmasker NM_00113*
   repeatmasker NM_00114*
   repeatmasker NM_00115*
   repeatmasker NM_00116*
   repeatmasker NM_00117*
   repeatmasker NM_00118*
   repeatmasker NM_00119*
   

2. Submit this job with:

   swarm -f swarmcmd
   

Example 3: Setting up your own programs for large-scale analysis

Swarm

#
# this file is cmdfile
#
myprog -param a < infile-a > outfile-a
myprog -param b < infile-b > outfile-b
myprog -param c < infile-c > outfile-c
myprog -param d < infile-d > outfile-d
myprog -param e < infile-e > outfile-e
myprog -param f < infile-f > outfile-f
myprog -param g < infile-g > outfile-g

2. Submit the job via the 'swarm' command.

swarm -f cmdfile

Example 4: Linkage Analysis using Parallel Genehunter

#!/bin/bash -v
# This file name is my_script
#
#PBS -N run1
#PBS -m be
#PBS -k oe

PATH=/usr/local/mpich/bin:$PATH; export PATH

mpirun -machinefile $PBS_NODEFILE -np $np ght < test.in

qsub -l nodes=1 my_script

biobos% qsub -I -l nodes=1
qsub: waiting for job 664776.biobos to start
qsub: job 664776.biobos ready

[user@p2 ~]$ cd /data/username/mydir
[user@p2 mydir]$ setenv PATH /usr/local/mpich/bin:$PATH
[user@p2 mydir]$ mpirun -machinefile $PBS_NODEFILE -np 1 /usr/local/bin/ght < test.in


************************************************************************
*                                                                      *
*        GENEHUNTER-TWOLOCUS - A modified version of GENEHUNTER        *
*                             (version 1.3)                            *
*                                                                      *
************************************************************************

Type 'help' or '?' for help.
Can't find help file - detailed help information is not available.
See installation instructions for details.

 running on 1 nodes

npl:1> 'photo' is on: file is 'two02.out'

npl:2> Fri Nov 25 13:54:28 2005

npl:3> Single point mode is now 'off'

npl:4> Count recs is now 'off'

npl:5> Haplotype output is now 'off'

npl:6> Unaffected children are now used.

npl:7> Currently analyzing a maximum of 9 bits per pedigree

npl:8> Large pedigrees are now used but trimmed.

npl:9> The current analysis type is 'BOTH'
 [...]

[user@p2 /data/user/mydir] exit
logout

qsub: job 668223.biobos completed
[susanc@biobos ~]$

You must exit the node after an interactive run!

Databases

URLs