AUGUSTUS Forum

Originally posted in the old forum by Clement on 16.10.2014 - 19:19 Hi all, I'm using Augustus for gene prediction in a new species. Both the genome and the hint file are home-made. When running autoAugTrain.pl, i get the following error message : ERROR: training.gb is empty. Possible reasons: a) f...

by Katharina on 22.07.2015 - 09:17 This may happen if you filter for pairedness but the "paired format" is not supported by filterBam. Have you compared the format of your input file to the format instructions at http://bioinf.uni-greifswald.de/bioinf/wiki/pmwiki.php?n=IncorporatingRNAseq...

by Willow on 22.07.2015 - 02:21 I have another question about filterBam. When I run filterBam with the command /home/jjian/augustus-3.1/auxprogs/filterBam/bin/filterBam --uniq --paired --in accepted_hits.s.bam --out accepted_hits.sf.bam it aborted after running several hours and told me [1]+ Aborte...

by Willow on 21.07.2015 - 04:11
Oh, the bin directory is created!And filterBam can run successfully!Thank you very much!

by Willow on 21.07.2015 - 04:08 When I remove all *.o files in filterBam directory and src directory,and type make, it returns: make[1]: Entering directory `/home/jjian/augustus-3.1/auxprogs/filterBam/src' g++ -I/home/jjian/bamtools-2.3.0/include -Iheaders -I/home/jjian/bamtools-2.3.0/src/toolkit -...

by katharina on 20.07.2015 - 11:48
Then please remove the pre-compiled *.o files and try again.

by Willow on 20.07.2015 - 09:24
No，I did not remove any files of filterBam

by Katharina on 08.07.2015 - 15:49
Another question: did you remove the pre-existing *.o files of filterBam prior your attempt to compile?
I am wondering because your output seems to show the linking process, only, not the compiling process.

by Willow on 03.07.2015 - 13:33 I download bamtools-2.3.0，and try to compile filterBam, but it still returns： make[1]: Entering directory `/home/jjian/augustus-3.1/auxprogs/filterBam/src' g++ -I/home/jjian/bamtools-2.3.0/include -Iheaders -I/home/jjian/bamtools-2.3.0/src/toolkit -std=c++0x filterBa...

by Katharina on 02.07.2015 - 08:50 Please try bamtools 2.3.0. That's the last bamtools version that I verified fitlerBam to run with. (We will look into why it's not working with 2.4.0, but that might take a while since the developer of filterBam is not longer working in our group.) Best, Katharina

Originally posted by Willow in the old forum on 01.07.2015 - 15:42

bamtools-2.4.0

Originally posted by Katharina in the old forum on 01.07.2015 - 11:56

Which version of bamtools did you use?

Originally posted by Willow in the old forum on 01.07.2015 - 11:04 After install bamtools successfully,I change directory to filterBam, and type make,but it returns： (cd src;make) make[1]: Entering directory `/home/jjian/augustus-3.1/auxprogs/filterBam/src' g++ -I/home/jjian/bamtools-master/include...

AutoAug.pl will not be able to use all that evidence, directly.

You could feed ESTs (or proteins) for training and convert all other evidence to hints, manually. You might want to modify the extrinsic.cfg file to your needs.

Originally posted by adnguyen in the old forum on 10.01.2014 - 15:20 Hi Katharina, Could you please give me some advice how to train my data using autoAug.pl script (I prefer not to submit my data to your web service). I have the following data of a genome: - ESTs - RACE - proteins - RNA-Seq and Tr...

Originally posted by tnguyen in the old forum on 15.10.2012 - 14:48

Thank you Katharina.
T

Originally posted by katharina in the old forum on 10.10.2012 - 21:32 In this case, I recommend that you submit your data to our web service at http://bioinf.uni-greifswald.de/webaugustus Submit the genome and protein file. After the jobs finished, you'll be able to download a parameter archive tha...

Originally posted by tnguyen in the old forum on 10.10.2012 - 00:08

Thank you Kathrina,

I did add the PATH as follows:
PATH="/group/aquaculture/mussels/sequencing/programs/Scipio/scipio-1.4:$PATH"
export PATH

and it is not working still.

Originally posted by katharina in the old forum on 09.10.2012 - 20:18 Did you add Scipio to your path variable? Please add the path to the scipio executable to your PATH, e.g. in the .bashrc or in your .profile file. If you keep on working on the same shell after adding it, you need to reload the ....

Originally posted by tnguyen in the old forum on 09.10.2012 - 10:03 Dear all, I am new to AUGUSTUS, and would be grateful if you could help. I have a genome of a non-model organism and would like to predict genes from the genome. 1. I have downloaded EST database from the same species and closely r...