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kelkar / Discover_pseudogenes

Discover pseudogenes in a newly assembled genome, using reference gene/protein sequences.
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Exonerate step #1

Open suba19997 opened 3 months ago

suba19997 commented 3 months ago 

This command results in KILLED message and it is not successful in ubuntu. What could be the reason? If storage/ RAM space is the reason, then what can be the solution?Is there any other way to generate this output.
suba19997 commented 3 months ago 

exonerate --percent 60 --model protein2genome --showquerygff yes --showtargetgff yes -q QUERY_PROTEINS.fasta -t TARGET_GENOME.fasta --ryo "RYO\t%qi\t%ti\t%ql\t%tl\t%qal\t%qab\t%qae\t%tal\t%tab\t%tae\t%et\t%ei\t%es\t%em\t%pi\t%ps\t%g\nTransitionStart\n%V{%Pqs\t%Pts\t%Pqb\t%Pqe\t%Ptb\t%Pte\t%Pn\t%Pl\n}TransitionEnd\nTargetSeq\n%qs\nAligned Sequences\n>Q\n%qas\n>T\n%tas\nCoding Sequences\n>Q\n%qcs\n>T\n%tcs\n" >  EXONERATE_OUTPUT.TXT