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Old 03-24-2013, 06:43 AM   #1
yzzhang
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Location: florida

Join Date: Jan 2013
Posts: 67
Unhappy augustus could not run, scipio possible not in path

Hi, all.
Now I am annotating a plant genome. At first I annotated it using maker pipeline with SNAP to denovo predicate genes. Finally I got some protein and transcript sequeces, but only about ~40% proteins were both supported by maker and SNAP, so I want to use these proteins both supported by maker and SNAP to train augustus and improve the prediction.
I used augustus 2.7. and run with parameter : ./autoAug.pl --species=myspecies --genome=mygenome_masked --cdna=trinity_assembly --trainingset=snap_masked_maker.fa, then I got the error: Program aborted. Possibly "scipio" is not installed or not in your PATH at /home/zhang/software/augustus.2.7/scripts/autoAugTrain.pl line 826.
I am sure scipio.1.4 is in my path, and I can run it successfully. So I am confused, because I am not good at perl, I don't know how to fix this problem. Did anybody face with this problem? How did you fix it? Many Thanks.
Best Wishes,
yunz
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Old 03-24-2013, 08:11 PM   #2
mike.t
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Location: Spain

Join Date: Mar 2010
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I'd recommend using the web service for training augustus instead:
http://bioinf.uni-greifswald.de/trainaugustus
It worked great for us.

Mike
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