Probably your perl or Getopt::Long module is out of date - change the relevant option description line in the process_exonerate_gff3.pl script (line 117 in the version I just downloaded) from: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.

Chris

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.

I used exonerate2hints.pl, 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.