Question: Process_Exonerate_Gff3.Pl Error
gravatar for Bruno
7.6 years ago by
Bruno10 wrote:

I am trying to use the script, which converts exonerate output into gff format. Whatever I do the script returns the following error message:

Error in option spec: "gff_version|gf|v|:s"

For instance, I am using the following syntax:

perl -t Protein infile.txt > out.gff3

the error message is produced even if I invoke the help

perl -h

all perl modules required are installed

perl gene gff • 1.9k views
ADD COMMENTlink modified 7.5 years ago by Lhl730 • written 7.6 years ago by Bruno10
gravatar for Chris Penkett
7.6 years ago by
Chris Penkett480
Cambridge, UK
Chris Penkett480 wrote:

Probably your perl or Getopt::Long module is out of date - change the relevant option description line in the script (line 117 in the version I just downloaded) from:

'gff_version|gf|v|:s' => $gff_ver,

to something like:

'gff_version:s' => $gff_ver,

It's also possible that the options on lines 109 and 110 will cause similar issues.


ADD COMMENTlink written 7.6 years ago by Chris Penkett480
gravatar for Neilfws
7.5 years ago by
Sydney, Australia
Neilfws48k wrote:

You may have an old version of the script. There's a Sourceforge version (currently 3 years old) and a more recent Github version.

Note also the documentation near the top of the latter version, which states that exonerate must have been run with certain options for the script to work.

ADD COMMENTlink written 7.5 years ago by Neilfws48k
gravatar for Lhl
7.2 years ago by
United States
Lhl730 wrote:

I used, which comes along with augustus.

However, i found it worked only when i produced gff files using --model protein2genome. When switching to --model est2genome, this script does work any longer.

ADD COMMENTlink written 7.2 years ago by Lhl730
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