Question: Convert exonerate output to EVM gff3 format error
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gravatar for sun.nation
3.4 years ago by
sun.nation120
United States
sun.nation120 wrote:

Hello,

Exonerate command:

exonerate --model est2genome --showvulgar no --showalignment no --showquerygff no --showtargetgff yes --percent 80  --softmasktarget yes -q transcripts.fasta -t genome.fasta  > exonerate.gff

I used command provided by EVM to convert to gff3:

exonerate_gff_to_alignment_gff3.pl exonerate.gff3

Error:

Error, line has unexpected format: Chr_01       exonerate:est2genome    gene    769406  770204  2591    -       .       gene_id 1 ; sequence CBOT101-C20 ; gene_orientation + at /home/user/bin/EVM_r2012-06-25/EvmUtils/misc/exonerate_gff_to_alignment_gff3.pl line 57, <$fh> line 31.

There is same error when used with exonerate output file provided as example in EVM.

Thanks

SS

ADD COMMENTlink modified 3.4 years ago by Daniel Standage3.8k • written 3.4 years ago by sun.nation120

Welcome to BioStar! Hmm, yes, the error message is a bit cryptic. Two comments: first, I would check to make sure that exonerate ran correctly and had no error messages; second, if indeed there were no errors when you ran exonerate, I would recommend contacting the EVM developer Brian Haas. In my experience he is very responsive, and since this error message is so vague, he may be in a better position to help you.

Hope this helps!

ADD REPLYlink written 3.4 years ago by Daniel Standage3.8k
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