AUGUSTUS Forum

Posted: **Thu Nov 19, 2015 2:40 pm**

Originally posted by Marie in the old forum on 03.11.2014 - 16:22

Hello,
I am using autoAug.pl to train Augustus on a new species.
However, there is an error :

Code: Select all

augustus --species=myspecies /Data/Genomics/GeneAnnotation/Maker_pipeline/3_Train_Augustus/Using_M
aker/Training2/autoAug/autoAugTrain/training/training.gb.test > /Data/Genomics/GeneAnnotation/Maker_pipeline/3_Train_Augustus/Using_Maker/Training2/autoAug/autoAugTrain/training/test/augustus.1.out

augustus: ERROR
	Could't open the file with transition probabilities.

I checked that the directory myspecies exists in the augustus/species directory and that the matrix file is here (as well as pbl and cfg). It's all ok !
So I don't understand WHERE Augustus is looking for this file ?
Thank you !
Marie

Posted: **Thu Nov 19, 2015 2:40 pm**

Originally posted by Marie in the old forum on 04.11.2014 - 16:37

Hey !
I found a way to fix this problem.
From the beginning, the script looks for information in augustus/bin/model and augustus/bin/species rather than in augustus/config.
So I copied myspecies/ and model/ directories from config to bin.
However, I hope that augustus will always look for info in bin rather than in config, because the config files won't be updated at the end of the training, only those found in bin...
Any advice ?
Thank you !
Marie

Posted: **Thu Nov 19, 2015 2:41 pm**

You can set your customized AUGUSTUS_CONFIG_PATH variable that points to the location of your config files. Either set it in your .bashrc/.profile file, or add it as a command line argument to each augustus call.

AUGUSTUS Forum

Problem with autoAug.pl : transition file not found ???

Problem with autoAug.pl : transition file not found ???

Re: Problem with autoAug.pl : transition file not found ???

Re: Problem with autoAug.pl : transition file not found ???