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Old 01-23-2015, 07:42 PM   #1
sandesh
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Default exonerate - how to use multiple cores?

Hello,
I used this command to run exonerate:

exonerate -m p2g -q uniref90_modified.fasta -t all_LGs/PcapLG_18.fasta --softmasktarget yes --showvulgar no --showalignment no --showtargetgff yes --showquerygff no --percent 80 " > LG18_exonerate_pcap.gff

This only use one core. I have 32 cores.
It's getting too slow.

Thanks
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Old 01-23-2015, 09:02 PM   #2
atcghelix
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I would try running it in server-client mode:

http://i.animalgenome.org/bioinfo/re...te/server.html
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Old 01-25-2015, 08:38 AM   #3
sandesh
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I tried exonerate-server too. This one is also slow.
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Old 01-27-2015, 12:39 AM   #4
Blahah404
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exonerate is simply a slow program. You can split the query file up into 32 files and run 32 exonerate commands simultaneously, then concatenate the results.

exonerate comes with a a tool, fastasplit, for this purpose
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Old 01-27-2015, 05:47 AM   #5
sandesh
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Quote:
Originally Posted by Blahah404 View Post
exonerate is simply a slow program. You can split the query file up into 32 files and run 32 exonerate commands simultaneously, then concatenate the results.

exonerate comes with a a tool, fastasplit, for this purpose

Thanks
I tried that too. I made 100 parts. Running single file took more then 3 days and stopped, which means more then 300 days to go.
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Old 01-27-2015, 05:51 AM   #6
colindaven
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GMAP might be suitable for your purposes (transcript mapping to GFF3), and is a lot quicker with good parallelization.
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