AUGUSTUS Forum

Originally posted in the old forum by Rohit on 22.02.2015 - 18:33

Hello.
I tried to run augustus but had to increase the accuracy as it was low with under 20%.
So I tried to run optimise-augustus as
/scr/bloodymary/user/augustus-mito/scripts/optimize_augustus.pl --species=sam_mito refs_mito.gb --AUGUSTUS_CONFIG_PATH=/scr/bloodymary/user/augustus-mito/config/ --cpus=5
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augustus: ERROR
No sequences found.
8
starting accuracy: 0.0077, 0.9940, 0.0154, 0.6670, 0.0154, 0.6670, 0.00, 0.00, starting target: 0.4550
improving parameter /Constant/dss_end curently set to 4
1-4
/Constant/dss_end: checking values 1 2 3 4
bucket
etraining: ERROR
Input file not in genbank format.
augustus: ERROR
IntronModel::readProbabilities: Error reading file /scr/bloodymary/user/augustus-mito/config/species/sam_mito/sam_mito_intron_probs.pbl
Could not read the accuracy values out of predictions.txt when processing bucket 1. at /scr/bloodymary/user/augustus-mito/scripts/optimize_augustus.pl line 896.
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The genbank file is not empty, since when I run etraining and augustus later manually, they are able to detect the file.
I'm using the latest version (3.0.3) of augustus. Can I please know what the problem is?

by katharina on 23.02.2015 - 15:39

The first issue is very likely a genbank file format problem. etraining can be a bit more "tolerant" than optimize_augustus.pl.
Carefully compare the format of your file to the instructions at http://bioinf.uni-greifswald.de/webaugu ... #structure
Concerning the second issue, have you checked whether the file /scr/bloodymary/user/augustus-mito/config/species/sam_mito/sam_mito_intron_probs.pbl exists?
Katharina