AUGUSTUS Forum

hi all,
I only used the protein to train Augustus.
The command:
perl autoAug.pl --genome=named.fasta--species=name --useexisting -v -v -v --noutr --workingdir=/path/to/workingdir/ --trainingset=protein.fasta 2> Aug.log
The error is:
Program aborted. Possibly "scipio" is not installed or not in your PATH at /augustus/augustus-3.0.1/scripts/autoAugTrain.pl line 829.
failed to execute: No such file or directory
Then I check the line 829 :
$cmdString = "scipio.pl $genome $trainingset > scipio.yaml 2> scipio.err";
print "3 $cmdString ..." if ($verbose>2);
system("$cmdString")==0 or die("Program aborted. Possibly \"scipio\" is not installed or not in your PATH");

But I am pretty sure that I add Scipio to my path. Because I do can run the commond "scipio.pl $genome $trainingset > scipio.yaml 2> scipio.err" .I don't know why Scipio won't work when running the autoAug.pl .

Your help will be much appreciated.

Hi @eggland

I'm having exactly the same issue. The weirdest part is that I do see that scipio.pl is doing something because a file Scipio30701_blat.psl is created and filled with alignments for like about an hour before it complains suddenly that scipio.pl is not in my path (but it is).

Have you found any solution?

Thanks!

Hi,

I apologize that AutoAug.pl still produces this unspecific error message! (We will - hopefully - fix that one day...)

The problem you are facing is that the output of

scipio.pl $genome $trainingset > scipio.yaml 2> scipio.err

does not contain what AutoAug.pl expects.

Most often, this happens when scipio did not produce any output, at all. Check scipio.yaml whether it contains an output. If not, check scipio.err, whether scripio had any issues. If yes, fix those issues and try again. If not, scipio simply was not able to produce gene structures.

Katharina