Search found 12 matches

by Admin
Thu Nov 19, 2015 2:19 pm
Forum: Predicting Genes with AUGUSTUS
Topic: FeatureCollection::esource: invalid source key: E
Replies: 5
Views: 2726

Re: FeatureCollection::esource: invalid source key: E

Originally posted by mario in the old forum on 09.10.2014 - 17:10 We don't have a parameter for that (there are already >200 command line parameters) but you can simply edit the source code file src/gene.cc. Go to the function Evidence::print() change the number in the expression grouplistlen < 80 ...
by Admin
Thu Nov 19, 2015 2:18 pm
Forum: Predicting Genes with AUGUSTUS
Topic: FeatureCollection::esource: invalid source key: E
Replies: 5
Views: 2726

Re: FeatureCollection::esource: invalid source key: E

Originally posted by Mbandi in the old forum on 09.10.2014 - 12:41 For genes that were predicted with hints, I would like to generate the list of all hints per gene. The output of AUGUSTUS seems to truncate the list of hints when it is long. For example 1. hint groups fully obeyed: 5 2. XNT: 5 (T_c...
by Admin
Thu Nov 19, 2015 2:18 pm
Forum: Predicting Genes with AUGUSTUS
Topic: FeatureCollection::esource: invalid source key: E
Replies: 5
Views: 2726

Re: FeatureCollection::esource: invalid source key: E

Originally posted in the old forum by katharina on 07.10.2014 - 09:33 AUGUSTUS is build to predict genes ab initio (i.e. where there is no evidence at all), but if you add evidence, it will use the evidence where it is available. You can filter the predictions for genes without evidence (under each...
by Admin
Thu Nov 19, 2015 2:17 pm
Forum: Predicting Genes with AUGUSTUS
Topic: FeatureCollection::esource: invalid source key: E
Replies: 5
Views: 2726

Re: FeatureCollection::esource: invalid source key: E

Originally posted by Mbandi in the old forum on 06.10.2014 - 11:39

With external evidence available as hints, it appears AUGUSTUS will predict genes even in regions with not evidence. Is there a flag to turn off this behaviour?
by Admin
Thu Nov 19, 2015 2:17 pm
Forum: Predicting Genes with AUGUSTUS
Topic: FeatureCollection::esource: invalid source key: E
Replies: 5
Views: 2726

Re: FeatureCollection::esource: invalid source key: E

Originally posted by mario in the old forum on 18.03.2012 - 12:20 The problem is probably that you are using the default extrinsic.cfg file in the folder config/extrinsic that does not know the source key E. Copy one of the extrinsic.cfg example files from this folder that contains E in the line af...
by Admin
Thu Nov 19, 2015 2:16 pm
Forum: Predicting Genes with AUGUSTUS
Topic: FeatureCollection::esource: invalid source key: E
Replies: 5
Views: 2726

FeatureCollection::esource: invalid source key: E

Originally posted by njauxiongjie in the old forum on 18.03.2012 - 12:19 I have aligned my EST to my genome and want to use the EST alignment as hints of augustus. The command I run like your README file in AUGUSTUS, and like bellow: blat -minIdentity=92 genome.fa cdna.fa cdna.psl blat2hints.pl --i...
by Admin
Thu Nov 19, 2015 2:15 pm
Forum: AUGUSTUS Compilation/Installation
Topic: Trouble compiling augustus...
Replies: 5
Views: 3609

Re: Trouble compiling augustus...

Originally posted by Jackie in the old forum on 30.04.2013 - 05:51 Hi everyone, I don't get any error messages when I type "g++ -v". Although I'm still unable to compile augustus using "make", I was able to download augustus using maker, so... we'll call that a win for the momen...
by Admin
Thu Nov 19, 2015 2:15 pm
Forum: AUGUSTUS Compilation/Installation
Topic: Trouble compiling augustus...
Replies: 5
Views: 3609

Re: Trouble compiling augustus...

Originally posted by mario in the old forum on 29.04.2013 - 18:26

This has nothing to do with augustus itself. You have to make
sure that e.g. typing

Code: Select all

g++ -v 
on the command line does not give you an error on your system. g++ is the GNU C++ compiler.
by Admin
Thu Nov 19, 2015 2:14 pm
Forum: AUGUSTUS Compilation/Installation
Topic: Trouble compiling augustus...
Replies: 5
Views: 3609

Re: Trouble compiling augustus...

Originally posted by Jackie in the old forum on 29.04.2013 - 16:29

p.s. I should probably clarify that I downloaded and unpacked augustus.2.7, not augustus.2.5.5 as I originally wrote... otherwise everything I wrote above is correct.
Best wishes, Jackie
by Admin
Thu Nov 19, 2015 2:14 pm
Forum: AUGUSTUS Compilation/Installation
Topic: Trouble compiling augustus...
Replies: 5
Views: 3609

Re: Trouble compiling augustus...

Originally posted by Jackie in the old forum on 29.04.2013 - 16:19 Hi Katharina, Thanks for your response... I ran your command and it says "gcc is already the newest version" which I assume means it is installed. When I run "make" again I get the same error message I copied abo...
by Admin
Thu Nov 19, 2015 2:13 pm
Forum: AUGUSTUS Compilation/Installation
Topic: Trouble compiling augustus...
Replies: 5
Views: 3609

Re: Trouble compiling augustus...

Originally posted by katharina in the old forum on 29.04.2013 - 10:32

Have you installed the compiler on your system? Try "sudo apt-get install gcc".
Katharina
by Admin
Thu Nov 19, 2015 2:13 pm
Forum: AUGUSTUS Compilation/Installation
Topic: Trouble compiling augustus...
Replies: 5
Views: 3609

Trouble compiling augustus...

Originally posted by Jackie in the old forum on 29.04.2013 - 01:00 Hi! I have unpacked augustus.2.5.5.tar.gz to my usr/local directory. I can see the bin, config, docs, etc. subfiles in the directory. When I change into the src directory, however, and type "make" I get the following error...