Error: Possibly "scipio" is not installed or not in your PATH
Posted: Thu May 12, 2016 2:28 pm
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.
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.