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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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Originally posted by Blahah404 View Postexonerate 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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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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I would try running it in server-client mode:
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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.
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