A workflow that accelerates identification of ARG-like sequences with CARD RGI. Built and tested on GNU/Linux.
- Filter fasta sequences for those that contain possible ARGs
- Run RGI against the filtered fasta file
- Create fasta file for each ARO with all predicted ARGs
Usage: runner.py [OPTIONS] CONTIGS_FASTA
Analysis Workflow Management
Sets up Pyflow WorkflowRunner and launches locally by default or via flux
Options:
-r, --reference TEXT
-o, --output TEXT
--flux / --no-flux
--dispatch / --no-dispatch
-a, --account TEXT
-p, --ppn INTEGER
-m, --mem TEXT
-w, --walltime TEXT
--help Show this message and exit.
$ git clone https://github.com/jordangumm/arg_identifier.git
$ cd arg_identifier && ./build.sh
$ source ./dependencies/miniconda/bin/activate
$ python runner.py [CONTIGS_FASTA]
Depending on the size of the input fasta and/or reference, you may need to increase the memory --mem and processor count --ppn
$ source ./dependencies/miniconda/bin/activate
$ python runner.py [CONTIGS_FASTA] --flux --account [ACCOUNT]