PIRSF fails

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When I try to run the PIRSF algorithm on out SGE cluster, I get some java error 
caused by 

Caused by: java.io.IOException: java.io.IOException: error=2, No such file or 
directory
    at java.lang.UNIXProcess.<init>(UNIXProcess.java:148)
    at java.lang.ProcessImpl.start(ProcessImpl.java:65)
    at java.lang.ProcessBuilder.start(ProcessBuilder.java:453)

On a normal linux machine (on which I am a sudoer) I can fix this by installing 
ia32lib libraries

on  the cluster it is a simple matter of doing the following:
#binary.blastall.2.2.6.path=bin/blast/2.2.6/blastall
binary.blastall.2.2.6.path=bin/blast/2.2.19/blastall

it seems to work and avoids using decade old code.

Should this cause any problems?  could the 2.2.6 blast be done away with?

Original issue reported on code.google.com by jizosa...@gmail.com on 22 May 2013 at 9:33

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It could have an effect on the results you get. The PIRSF algorithm 
incorporates a BLAST step, which is used to filter the raw matches you get from 
the sequence search against an HMM database. PIRSF's suggestion is to use BLAST 
version 2.2.6. So therefore InterProScan 5 is restricted to use this version.
But based on our experience only a very tiny amount of sequences need to pass 
that BLAST step.

I think you would need to double check with the PIRSF guys 
(http://pir.georgetown.edu/pirwww/support/) what exactly effect a newer BLAST 
version would have and if it could be done without the BLAST step as well.

Kind Regards,
Maxim

Original comment by Maxim.Sc...@gmail.com on 23 May 2013 at 11:42

• Changed state: Started

[GoogleCodeExporter]

Thanks for the reply, I will post their answer to the query here.

Original comment by jizosa...@gmail.com on 23 May 2013 at 5:04

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Original comment by Maxim.Sc...@gmail.com on 11 Sep 2013 at 10:05

• Added labels: Subject-BLAST