meta data for this page
  •  

This is an old revision of the document!

InterPro

General information

To run InterPro locally, you need to download the InterPro databases and modify the configure file of the program. For your convenience, we prepared a ready to use version of InterProScan available at 

/share/project/interproscan-5.28-67.0

Please run it straight from the share folder and don't attempt to copy it. Because InterProScan takes up a lot of memory, you should send this job to our cluster:

Note, that InterProScan can not create folders for the output. That means that you need to use an existing directory that does not contain special characters like dots in its name for the output.

PrerequisitesInterproScan

PrerequisitesInterproScan

  1. Python 2.7
    1. you can check your python version with the command 
      python --version
  2. Java 1.8
    1. you can check your java version with the command 
      java -version

Running Interproscan 

bash /share/project/interproscan-5.28-67.0/interproscan.sh -i <YOURINPUTFILE> -b ./interproscan -goterms -appl TIGRFAM,PRODOM,PFAM,SMART,CDD,PROSITEPROFILES,PANTHER,Coils,MobiDBLite

Options:

  1. -i - specify the input file containing the sequences in Fasta format.
  2. -b - specify the name of the output directory
  3. -goterms - Extract the GO terms from the annotated domains and features and assigns them to the query sequence
  4. -appl - specify the analyses you want to include in your Interproscan run. Selecting fewer applications will speed up the search

For further information about how to run Interproscan, please see the online wiki provided by the developer.

Once everything is set, run the analysis on all sequences. This analysis will take some time, so you best run it over the weekend.

RunInterpro.sh
#!/bin/bash
 
#SBATCH --partition=all,inteli7
#SBATCH --cpus-per-task=8
#SBATCH --mem=10GB
#SBATCH --job-name="InterProTest"
 
 
bash /share/project/interproscan-5.28-67.0/interproscan.sh -i <YOURINPUTFILE> -b ./interproscan -goterms -appl TIGRFAM,PRODOM,PFAM,SMART,CDD,PROSITEPROFILES,PANTHER,Coils,MobiDBLite

Just download and modify this file, then send it to the cluster with 

sbatch RunInterpro.sh

Interproscan configuration

We have tweaked the configuration of interproscan a bit to improve the performance on our system. You will find the corresponding file at 

/share/project/interproscan-5.28-67.0/interproscan.properties

Specifically, we made the following changes

  • We have set the max number of workers to 2<WRAP>
## Master/Stand alone embedded workers
##

# Set the number of embedded workers to the number of processors that you would like to employ
# on the machine you are using to run InterProScan.
#number of embedded workers  a master process can have
number.of.embedded.workers=1
maxnumber.of.embedded.workers=2
  • and start hmmsearch and pfamscan with 3 cpus each
## cpu options for parallel processing
##

#hmmer cpu options for the different jobs
hmmer3.hmmsearch.cpu.switch.gene3d=--cpu 3
hmmer3.hmmsearch.cpu.switch.panther=--cpu 3
hmmer3.hmmsearch.cpu.switch.pfama=--cpu 3
hmmer3.hmmsearch.cpu.switch.pirsf=--cpu 3
hmmer3.hmmsearch.cpu.switch.sfld=--cpu 3
hmmer3.hmmsearch.cpu.switch.superfamily=--cpu 3
hmmer3.hmmsearch.cpu.switch.tigrfam=--cpu 3

hmmer3.hmmsearch.cpu.switch.hmmfilter=--cpu 3

hmmer2.hmmpfam.cpu.switch.smart=--cpu 3


#panther binary cpu options (for blastall and hmmsearch)
panther.binary.cpu.switch=-c 3

#pirsf binary cpu options (for hmmscan)
pirsf.pl.binary.cpu.switch=-cpu 3