Errors about exonerate gff2 file to EVM gff3 converting

Question

[Ginsea Chen]

Dear all

I used exonerate to map protein to genome with command:

exonerate \
  -q query.fa \
  -t genome.fa \
  --querytype protein \
  --targettype dna \
  --model protein2genome \
  --showtargetgff yes \
  --showquerygff no \
  --showalignment no \
  --showvulagr no \
  --showcigar no \
  --ryo no \
  --targetchunkid 1 \
  --targetchunktotal 10 > 1.gff

Then I used in-house Perl script of EVM to convert 1.gff file to EVM gff3 format, my command was a follows:

perl exonerate_gff_to_alignment_gff3.pl 1.gff prot >1.gff3.

While the terminal told me that

Can't use an undefined value as an ARRAY reference at /home/ginsea/Biosoftware/EVM/EvmUtils/misc/exonerate_gff_to_alignment_gff3.pl line 110, <$fh> line 37022.

And I checked 1.gff3 file. This file is not empty, but not contained all information of 1.gff file.

I don't know what happened, If any one have some suggestions, please tell me.

Thanks all!

[Juke34]

Could you display the line incriminated ?

line 37022 of 1.gff file

[Ginsea Chen]

Dear Juke-34

Thanks for you reply, I have solved this problem by using Exonerate_to_evm_gff3.pl (another Perl script of EVM).

Thanks!