Exonerate killed automatically

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4.7 years ago

ashaneev07 ▴ 40

Hiii... Exonerate stopped automatically after some time and get the output "Killed" on the terminal. Input file size given was 454 mb and protein file has 1 mb. The command that i've used is given below. So what would be the reason behind this? Can anyone please help me out of this? Thank you in advance.....

exonerate -t exseq.fa -q prot.fa --model protein2genome --showtargetgff 
--verbose 5 > initial.seq.gff

exonerate alignment next-gen • 1.9k views

ADD COMMENT • link 4.7 years ago by ashaneev07 ▴ 40

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Memory is typially the first of the usual suspects. How much RAM is available?

ADD REPLY • link 4.7 years ago by ATpoint 85k

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My system has 16 gb of RAM and now

free -m

        total        used        free      shared  buff/cache   available
Mem:          15928        2731       11912         126        1285       12790
Swap:          2047        1079         968

ADD REPLY • link 4.7 years ago by ashaneev07 ▴ 40

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How long did it run for? Are you running the task on the head node of a HPC scheduler?

ADD REPLY • link 4.7 years ago by Joe 21k

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It took around 20-30 mnts. My desktop detils is given below kindly check.

Memory 16 gb
OS typ 64-bit
os ubuntu 18.o4

ADD REPLY • link 4.7 years ago by ashaneev07 ▴ 40

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454 Mb of sequences sounds like quite a lot, how many sequences is that?

ADD REPLY • link 4.7 years ago by Joe 21k

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Hmm...it contains 6919 sequences. I was split the data into 4 (113 mb) but, that also shows the same error.

ADD REPLY • link 4.7 years ago by ashaneev07 ▴ 40

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Any guesses ? !!! .............

ADD REPLY • link 4.7 years ago by ashaneev07 ▴ 40

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I would re-run it and monitor memory usage. Probably you ran out of memory. Maybe try with like 10 sequences to see if it is a general problem.

ADD REPLY • link 4.7 years ago by ATpoint 85k

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