The HH-suite is an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs).

References:

• M. Remmert, A. Biegert, A. Hauser, J. Söding. HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment. Nature Methods 2011, 9:173-175. doi:10.1038/nmeth.1818

• hhsuite Main Site
• User Guide

• Module Name: hhsuite (see the modules page for more information)
• hhsuite is a multithreaded application. Make sure to match the number of cpus requested with the number of threads.
• Environment variables set
  • HHLIB
• Example files in /fdb/hhsuite/test-data
• Reference data in /fdb/hhsuite/

hhblits and hhsearch need to do many random file access and read operations. The central file systems (i.e. /data, /scratch, or /fdb) will not perform well under this type of load. This means that running against the database directly stored on /fdb will not be performant. In addition it may tax the file system enough to also slow down other user's computations. We therefore recommend to copy the database to be searched to lscratch. In particular, nodes with SSD storage should be used. This means that the ideal usage pattern for large hhblits/hhsearch jobs is to allocate a node (or nodes) exclusively, copy the database to lscratch, and then run all computations on that node.

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive --constraint=ssd3200 --gres=lscratch:100 --cpus-per-task=10
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 hhsuite
[+] Loading gcc  7.3.0  ... 
[+] Loading openmpi 3.0.0  for GCC 7.3.0 
[+] Loading hhsuite  3.3.0 
[user@cn3144 ~]$ cd /lscratch/$SLURM_JOB_ID
[user@cn3144 46116226]$ cp -r /fdb/hhsuite/uniprot20_2016_02 .
[user@cn3144 46116226]$ hhblits \
 -cpu $SLURM_CPUS_PER_TASK \
 -i /fdb/hhsuite/test-data/query.a3m \
 -d uniprot20_2016_02/uniprot20_2016_02 \
 -o query.hhr

- 17:04:47.198 INFO: Searching 8290206 column state sequences.

- 17:04:47.723 INFO: /fdb/hhsuite/test-data/query.a3m is in A2M, A3M or FASTA format

- 17:04:47.794 INFO: Iteration 1

- 17:04:48.727 INFO: Prefiltering database

- 17:06:47.000 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment)  : 302479
...
...
[user@cn3144 46116226]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. hhblits.sh). For example:

#!/bin/sh
set -e

module load hhsuite
cd /lscratch/$SLURM_JOB_ID
cp -r /fdb/hhsuite/uniprot20_2016_02 .

hhblits -i /fdb/hhsuite/test-data/query.seq \
  -d ./uniprot20_2016_02/uniprot20_2016_02 \
  -cpu $SLURM_CPUS_PER_TASK -o test.hhr \
  -oa3m test.a3m -n 6

hhmake -i test.a3m -o test.hhm
addss.pl test.hhm test_addss.hhm -hmm
cp test* /path/to/output/dir

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=6 --gres=lscratch:100 [--mem=#] hhblits.sh

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

cp -r /fdb/hhsuite/uniprot20_2016_02 /lscratch/$SLURM_JOB_ID \
&& hhblits -i sample1.seq -d /lscratch/$SLURM_JOB_ID/uniprot20_2016_02/uniprot20_2016_02 -cpu $SLURM_CPUS_PER_TASK -o sample1.hhr
cp -r /fdb/hhsuite/uniprot20_2016_02 /lscratch/$SLURM_JOB_ID \
&& hhblits -i sample2.seq -d /lscratch/$SLURM_JOB_ID/uniprot20_2016_02/uniprot20_2016_02 -cpu $SLURM_CPUS_PER_TASK -o sample2.hhr
cp -r /fdb/hhsuite/uniprot20_2016_02 /lscratch/$SLURM_JOB_ID \
&& hhblits -i sample3.seq -d /lscratch/$SLURM_JOB_ID/uniprot20_2016_02/uniprot20_2016_02 -cpu $SLURM_CPUS_PER_TASK -o sample3.hhr
cp -r /fdb/hhsuite/uniprot20_2016_02 /lscratch/$SLURM_JOB_ID \
&& hhblits -i sample4.seq -d /lscratch/$SLURM_JOB_ID/uniprot20_2016_02/uniprot20_2016_02 -cpu $SLURM_CPUS_PER_TASK -o sample4.hhr

Submit this job using the swarm command.

swarm -f hhblits.swarm [-g #] -t 6 --gres=lscratch:100 --module hhsuite