Biowulf High Performance Computing at the NIH
metamorpheus on Biowulf

MetaMorpheus is a bottom-up proteomics database search software with integrated post-translational modification (PTM) discovery capability. The HPC version do not provide GUI interface, and the toml files should be generated by Windows GUI first.

Features

References:

Documentation
Important Notes

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 input in bold):

[user@biowulf]$ sinteractive --cpus-per-task=4 --mem=5G
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 metamorpheus
[user@cn3144 ~]$ mkdir -p ~/mmconfig
[user@cn3144 ~]$ cp -r ${MM_CONFIG:-none}/* ~/mmconfig/
[user@cn3144 ~]$ metamorpheus --mmsettings ~/mmconfig --help
Welcome to MetaMorpheus

CMD 1.0.0

  -t              Single-task TOMLs (.toml file format); space-delimited
  -d              Protein sequence databases (.fasta, .xml, .fasta.gz, .xml.gz
                  file formats); space-delimited
  -s              Spectra to analyze (.raw, .mzML, .mgf file formats);
                  space-delimited
  -o              [Optional] Output folder
  -g              [Optional] Generate default task tomls
  -v              (Default: normal) [Optional] Determines how much text is
                  written. Options are no output ('none'), minimal output and
                  errors  ('minimal'), or normal ('normal')
  --test          [Optional] Runs a small test search using a database and yeast
                  data file included with this MetaMorpheus installation
  --mmsettings    [Optional] Path to MetaMorpheus settings
  --help          Display this help screen.
  --version       Display version information.


[user@cn3144 ~]$ metamorpheus --mmsettings ~/mmconfig --test -o test.out
[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. metamorpheus.sh). For example:

#!/bin/bash
#SBATCH --job-name=S1_metamorf
#SBATCH --output=S1_metamorf.out
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=10
#SBATCH --mem=10Gb
#SBATCH --time=8:00:00
#SBATCH --partition=norm

set -e
module load metamorpheus
cp -r ${MM_TEST_DATA:-none}/MetaMorpheusVignette /data/$USER/
cd /data/$USER/MetaMorpheusVignette

metamorpheus \
--mmsettings ~/mmconfig \
-t Task1-SearchTaskconfig.toml Task2-CalibrateTaskconfig.toml \
Task3-SearchTaskconfig.toml Task4-GPTMDTaskconfig.toml \
Task5-SearchTaskconfig.toml -s 04-30-13_CAST_Frac4_6uL.raw 04-30-13_CAST_Frac5_4uL.raw \
-d ./FASTA/uniprot-mouse-reviewed-2-5-2018.fasta

Submit the job:

sbatch metamorpheus.sh
Swarm of Jobs
A swarm of jobs is an easy way to submit a set of independent commands requiring identical resources.