This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Exonerate killed automatically

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
• 2,656 views • link
written by ashaneev07 • ashaneev07

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

• 0 views • link
written by ATpoint ATpoint

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
• 0 views • link
written by ashaneev07 • ashaneev07

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

• 0 views • link
written by Joe Joe

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
• 0 views • link
written by ashaneev07 • ashaneev07

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

• 0 views • link
written by Joe Joe

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

• 0 views • link
written by ashaneev07 • ashaneev07

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.

• 0 views • link
written by ATpoint ATpoint

0 answers

No answers yet.

Log in to answer this question.

More posts like this
  • Exonerate command in Ubuntu
    written by subashini.fbtpb106 • subashini.fbtpb106
    I am using exonerate command in the pseudogene pipeline https://github.com/kelkar/Discover_pseudogenes. But the command results in KILLED message and it is not successful in ubuntu. What …
  • question of exonerate output
    written by TN • TN
    I have a problem about gene annotation with software exonerate. I have a scaffold-level genome sequence (fasta, about 800Mb) of target species and protein sequences …
  • How to convert exonerate C4 alignment output to gff?
    written by Junior • Junior
    Hey guys, I run exonerate with the following settings: exonerate -t file1.fasta -q file2.fasta --model protein2genome --bestn 1 --ryo ">%qi %qd\n%qas\n" --showquerygff yes --maxintron 30000 …
  • Something wrong with my Exonerate gff
    written by Mike • Mike
    Hey all, I used the following command to align my proteome to genome: > exonerate --model protein2genome --showvulgar no --showalignment no --showtargetgff yes --percent 70 …
  • Homology based gene prediction
    written by bio_d • bio_d
    I am trying gene identification and annotation of a draft genome (de novo assembly) of a non-model species. I have downloaded protein (fasta) files of …
  • Segmentation fault (core dumped)
    written by Kumar Kumar
    I have been using fastANI tool to calculate Average Nucleotide Identity (ANI) value of multiple bacterial genome for the past 5 months. But recently I …
  • Error while running gatk
    written by ashaneev07 • ashaneev07
    Hiii Can anyone please help me to find a solution for this...I got the following error while running gatk for variant filtering. home@home-Lenovo-H30-50:~/Documents/Tools_NGS/gatk-4.0.6.0$ ./gatk VariantFiltration …
  • Several exonerate options; which to choose?
    written by mforthman • mforthman
    I am wanting to identify exon-intron boundaries between transcripts and a genome for a given species using exonerate. For the transcripts, I have both a …
  • Errors about exonerate gff2 file to EVM gff3 converting
    written by Ginsea Chen Ginsea Chen
    Dear all I used exonerate to map protein to genome with command: ``` exonerate \ -q query.fa \ -t genome.fa \ --querytype protein \ --targettype …
  • Exonerate Protein2Dna:Bestfit Problem
    written by Woa Woa
    <p>Hello.</p> <p>I'm having a problem to run the "protein2dna:bestfit" model in my 64 bit computer and under both Linux Cluster and Cygwin. For the Linux …