FeGenie

Overview

FeGenie uses this HMM library to search across provided datasets, and identifies potential homologs and operons that may be linked to the microbial iron cycle. Results are summarized in several output files, which include a master summary file, in which users can view the iron genes and iron gene operons that are present in their datasets, and a heatmap-compatible CSV file that summarizes the proportion of each genome that is dedicated to a particular iron-related function.

The source code master branches as of 3-Nov-2020 (github checksum c2a4b2d) and 25-Sept-2019 (github checksum b3c7057) are installed on the CSF.

Restrictions on use

There are no restrictions on accessing this software on the CSF.

Please cite your usage of the software using the references found on the FeGenie Github page.

Set up procedure

We now recommend loading modulefiles within your jobscript so that you have a full record of how the job was run. See the example jobscript below for how to do this. Alternatively, you may load modulefiles on the login node and let the job inherit these settings.

Load one of the following modulefiles:

module load apps/python/fegenie/201103
module load apps/python/fegenie/190925

FeGenie will use a number of external tools. Hence the above modulefile will automatically load the following modulefiles for you:

apps/anaconda3/5.2.0
apps/gcc/prodigal/2.6.3
apps/gcc/hmmer/3.2.1
apps/binapps/blast/2.9.0
apps/binapps/diamond/0.9.26
apps/R/3.5.3

To see a list of flags accepted by the FeGenie python script, you may run the following command:

FeGenie.py -h

However FeGenie should not normally be run on the login node. It should be noted that some flags, i.e -hmm_lib:

FeGenie.py -hmm_lib $FEGENIE_HDIR

do not exist on the later 201103 version.

Running the application

Please do not run FeGenie on the login node. Jobs should be submitted to the compute nodes via batch.

Serial batch job submission

Create a batch submission script (which will load the modulefile in the jobscript), for example:

#!/bin/bash --login
#$ -cwd             # Job will run from the current directory
                    # NO -V line - we load modulefiles in the jobscript

module load apps/python/fegenie/201103

# The $NSLOTS flag is automatically set to 1 for a serial (1-core) job.
FeGenie.py -bin_dir inputdir -bin_ext txt -out resultsdir -t $NSLOTS
   
   # If you wish to do plotting of results using R, add the following
   # flags to the above command:
   #
   # -R $FEGENIE_RDIR -makeplots y

Submit the jobscript using:

qsub scriptname

where scriptname is the name of your jobscript.

Parallel batch job submission