Question: Errors about exonerate gff2 file to EVM gff3 converting
0
gravatar for Ginsea Chen
2.9 years ago by
Ginsea Chen120
Chinese Academy of Tropical Agricultural Sciences, Danzhou, China
Ginsea Chen120 wrote:

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!

 

ADD COMMENTlink written 2.9 years ago by Ginsea Chen120

Could you display the line incriminated ?

line 37022 of 1.gff file

ADD REPLYlink written 2.9 years ago by Juke-341.3k

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!

ADD REPLYlink written 2.9 years ago by Ginsea Chen120
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