- Description
- InterProScan runs the scanning algorithms from the InterPro database in an integrated way.
- Modulefile
interproscan
- Documentation
- InterPro homepage
- Notes
- The precalculated match lookup service is not available from the compute nodes, and should be disabled with the
-dp
flag. See examples below.
- We do not support running InterProScan spanning multiple hosts (CLUSTER mode), but you can still run InterProScan on a single node with multiple CPU cores.
- Always submit your jobs with the request for 4 CPU cores, like so: "
-pe openmp 4
". The reason for this requirement is the fact that the software is centrally installed and users have no write access to the file interproscan.properties
, which sets the number of workers and threads as 2 by 2. According to our tests, Java's own overhead is minimal, and thus four CPU slots are adequate.
- Usage
- Here is an example of a submission script:
#$ -cwd
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G
#$ -pe openmp 4
module purge
module load gcc openmpi/gcc python/2.7.2 java interproscan
interproscan.sh -i $INTERPROSCAN/test_proteins.fasta -f tsv -dp
- Here is another example using a Local Scratch directory for temporary files:
#$ -cwd
#$ -l h_rt=1:0:0
#$ -l h_vmem=4G
#$ -pe openmp 4
module purge
module load gcc openmpi/gcc python/2.7.2 java interproscan
interproscan.sh -i 83333.fasta -dp -f tsv,html --goterms -T $TMPDIR