Combine GAFs on the ARS Ceres HPC

About Ceres/Scinet

Running GOanna on Ceres

Running programs on Ceres/Scinet

  • You’ll need to run combine_gafs either in interactive mode or batch mode.
  • For interactive mode, use the salloc command.
  • For batch mode, you’ll need to write a batch job submission bash script.

Running combine_gafs in interactive mode

Loading the module

The Scinet VRSC has installed the combine_gafs program. To load the module in interactive mode, run the command

module load agbase

Running Combine GAFs

Combine GAFs has three parameters:

-i InterProScan XML Parser GAF output
-g GOanna GAF output
-o output file basename

Example Command

combine_gafs -i CFLO_1.fa_gaf.txt -g clfo1_v_insecta_goanna_gaf.tsv -o complete_gaf
Command Explained

-i CFLO_1.fa_gaf.txt: InterProScan XML Parser GAF output file.

-g clfo1_v_insecta_goanna_gaf.tsv: GOanna GAF output file.

-o complete_gaf: output file basename–a .tsv extension will be added

Running combine_gafs in batch mode

Running programs on Ceres/Scinet in batch mode

Example batch job submission bash script (e.g. combine_gafs-job.sh):

#! /bin/bash
module load agbase
combine_gafs -i CFLO_1.fa_gaf.txt -g clfo1_v_insecta_goanna_gaf.tsv -o complete_gaf

Submitting the batch job:

sbatch combine_gafs-job.sh
Command Explained

-i CFLO_1.fa_gaf.txt: InterProScan XML Parser GAF output file.

-g clfo1_v_insecta_goanna_gaf.tsv: GOanna GAF output file.

-o complete_gaf: output file basename–a .tsv extension will be added