HMMER on Biowulf

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Profile hidden Markov models for biological sequence analysis

Profile hidden Markov models (profile HMMs) can be used to do sensitive database searching using statistical descriptions of a sequence family's consensus. HMMER uses profile HMMs, and can be useful in situations like:

if you are working with an evolutionarily diverse protein family, a BLAST search with any individual sequence may not find the rest of the sequences in the family.
the top hits in a BLAST search are hypothetical sequences from genome projects.
your protein consists of several domains which are of different types.

References:

HMMER (pronounced 'hammer', as in a more precise mining tool than BLAST) was developed by Sean Eddy at Washington University in St. Louis.

Documentation

The HMMER website is hmmer.janelia.org.
HMMER User Guide (PDF)

Important Notes

Module Name: hmmer (see the modules page for more information)
HMMER is a cpu-intensive program and is parallelized using threads, so that each instance of hmmsearch or the other search programs can use all the cpus allocated on a node.
An MPI version is also available, but given that most Biowulf nodes have 56 CPUs, only very large jobs may benefit from using the MPI version.
environment variables set
Example files in /usr/local/apps/hmmer/tutorial
Reference data in /fdb/fastadb/

Interactive job

Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive --cpus-per-task=16 --mem=10g
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load hmmer

[user@cn3144 ~]$ hmmsearch --cpu $SLURM_CPUS_PER_TASK /usr/local/apps/hmmer/tutorial/globins4.hmm /fdb/fastadb/nr.fas
# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.1b2 (February 2015); http://hmmer.org/
# Copyright (C) 2015 Howard Hughes Medical Institute.
# Freely distributed under the GNU General Public License (GPLv3).
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  /usr/local/apps/hmmer/tutorial/globins4.hmm
# target sequence database:        /fdb/fastadb/nr.fas
# number of worker threads:        16
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       globins4  [M=149]
[...]
  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 0.0014
        globins4  41 qefFekFkdLstedelkksadvkkHgkkvldAlsdalakld..ekleaklkdLselHakklkvdpkyfkllsevlvdvlaarlpkeftadvqaal 133
                     q++F++  +L+   ++   +     g+ + +A+++  +++d  + l ++++ ++++H ++++++ ++++++++ l+++l +  +  ft dv+ a
  WP_087017392.1  30 QRMFDHNPELKDIFNMSH-QRTGRQGVALFEAVAAYAKNIDnlGALTTAVERIAHKH-TSFNIQAEHYQIVGHHLIETLRELASDAFTKDVEEAW 122
                     677777777873333333.3345679999***********87889999*********.58*******************************9886 PP

        globins4 134 e 134

  WP_087017392.1 123 T 123
                     5 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                              1  (149 nodes)
Target sequences:                    145198384  (53182534605 residues searched)
Passed MSV filter:                   4463369  (0.0307398); expected 2903967.7 (0.02)
Passed bias filter:                  3672241  (0.0252912); expected 2903967.7 (0.02)
Passed Vit filter:                    255552  (0.00176002); expected 145198.4 (0.001)
Passed Fwd filter:                     17247  (0.000118782); expected 1452.0 (1e-05)
Initial search space (Z):          145198384  [actual number of targets]
Domain search space  (domZ):           10862  [number of targets reported over threshold]
# CPU time: 1306.00u 76.30s 00:23:02.30 Elapsed: 00:11:03.54
# Mc/sec: 11942.31

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Batch job

Most jobs should be run as batch jobs.

Create a batch input file (e.g. HMMER.sh). The following example uses the query sequence set globins4.hmm in the example directory, run against the NCBI nr protein database.

#!/bin/bash
set -e
module load hmmer
hmmsearch --cpu $SLURM_CPUS_PER_TASK /usr/local/apps/hmmer/tutorial/globins4.hmm /fdb/fastadb/nr.fas

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=16 --mem=10g HMMER.sh

Swarm of Jobs

A swarm of jobs is an easy way to submit a set of independent commands requiring identical resources.

Create a swarmfile (e.g. HMMER.swarm). For example:


hmmsearch --cpu $SLURM_CPUS_PER_TASK  file1.fas  /fdb/fastadb/nr.fas
hmmsearch --cpu $SLURM_CPUS_PER_TASK  file2.fas  /fdb/fastadb/nr.fas
hmmsearch --cpu $SLURM_CPUS_PER_TASK  file3.fas  /fdb/fastadb/nr.fas
[...]

Submit this job using the swarm command.

swarm -f HMMER.swarm -g 10 -t 32 --module hmmer

where

`-g #`	Number of Gigabytes of memory required for each process (1 line in the swarm command file)
`-t #`	Number of threads/CPUs required for each process (1 line in the swarm command file).
`--module hmmer`	Loads the HMMER module for each subjob in the swarm