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Old 01-23-2015, 09:44 AM   #1
Location: TN

Join Date: Jun 2013
Posts: 17
Default Exonerate uniref90.fasta alignment to 65MB genome


I was trying to align uniref90.fasta (10 gb) to genome for annotation.
I have 64 GB ram with 32 core.
It is already running since a month.
I was wondering if it is normal or there is other way to run quicker?

Thanks in advance
sandesh is offline   Reply With Quote
Old 01-23-2015, 11:33 AM   #2
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Location: East Coast USA

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A month already .. wow you are patient.

Are you sure something is happening as far as output being produced/CPU cycles being used productively?
GenoMax is offline   Reply With Quote
Old 01-23-2015, 12:00 PM   #3
Location: TN

Join Date: Jun 2013
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I used command below. uniref90 has got more then 22 M proteins.
I am not sure if the CPU are used properly.
I have been trying different ways like just running single scaffolds but run forever.
I am running this for EVM.
I also tried with targetchunk1-10 but no luck.

exonerate -m p2g -q uniref90_modified.fasta -t Pcap_genome.fasta --softmasktarget yes --showvulgar no --showalignment no --showtargetgff yes --showquerygff no --geneseed 200 --percent 80 --ryo "AveragePercentIdentity: %pi\n" > exonerate_pcap.gff

Please any suggestion.
sandesh is offline   Reply With Quote

alignment, evidencemodeler, exonerate, protein, uniref90

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