Exonerate uniref90.fasta alignment to 65MB genome

[sandesh]

Hello,

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

[GenoMax]

A month already .. wow you are patient.

Are you sure something is happening as far as output being produced/CPU cycles being used productively?

[sandesh]

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.