Hmmer

Introduction

Hmmer is used for searching sequence databases for sequence homologs, and for making sequence alignments.

For more information, please check:
BioContainers: https://biocontainers.pro/tools/hmmer
Home page: http://hmmer.org

Note

Please follow the recommended citation guidelines from the developers when you use the tool in research.

Versions

Cluster

Version(s)

ANVIL

3.3.2

BELL

3.3.2

GAUTSCHI

3.3.2

NEGISHI

3.3.2

SCHOLAR

3.3.2

Commands

  • alimask

  • easel

  • esl-afetch

  • esl-alimanip

  • esl-alimap

  • esl-alimask

  • esl-alimerge

  • esl-alipid

  • esl-alirev

  • esl-alistat

  • esl-compalign

  • esl-compstruct

  • esl-construct

  • esl-histplot

  • esl-mask

  • esl-mixdchlet

  • esl-reformat

  • esl-selectn

  • esl-seqrange

  • esl-seqstat

  • esl-sfetch

  • esl-shuffle

  • esl-ssdraw

  • esl-translate

  • esl-weight

  • hmmalign

  • hmmbuild

  • hmmconvert

  • hmmemit

  • hmmfetch

  • hmmlogo

  • hmmpgmd

  • hmmpgmd_shard

  • hmmpress

  • hmmscan

  • hmmsearch

  • hmmsim

  • hmmstat

  • jackhmmer

  • makehmmerdb

  • nhmmer

  • nhmmscan

  • phmmer

Module

You can load the modules by:

module load biocontainers
module load hmmer

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run hmmer on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -p wholenode        # Partition name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=hmmer
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers hmmer

# Your hmmer workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p cpu         # Partition name
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=hmmer
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers hmmer

# Your hmmer workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p ai          # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=hmmer
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers hmmer

# Your hmmer workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p a100        # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH --mem=2G       # Memory
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=hmmer
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers hmmer

# Your hmmer workflow...

#!/bin/bash
#SBATCH -A queue     # Queue name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=hmmer
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers hmmer

# Your hmmer workflow...