Search found 531 matches
- Thu Nov 19, 2015 2:58 pm
- Forum: WebAUGUSTUS
- Topic: formating the gff file
- Replies: 5
- Views: 10139
formating the gff file
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...
- Thu Nov 19, 2015 2:56 pm
- Forum: AUGUSTUS Compilation/Installation
- Topic: filterBam compiling error
- Replies: 11
- Views: 17365
Re: filterBam compiling error
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...
- Thu Nov 19, 2015 2:56 pm
- Forum: AUGUSTUS Compilation/Installation
- Topic: filterBam compiling error
- Replies: 11
- Views: 17365
Re: filterBam compiling error
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...
- Thu Nov 19, 2015 2:56 pm
- Forum: AUGUSTUS Compilation/Installation
- Topic: filterBam compiling error
- Replies: 11
- Views: 17365
Re: filterBam compiling error
by Willow on 21.07.2015 - 04:11
Oh, the bin directory is created!And filterBam can run successfully!Thank you very much!
Oh, the bin directory is created!And filterBam can run successfully!Thank you very much!
- Thu Nov 19, 2015 2:56 pm
- Forum: AUGUSTUS Compilation/Installation
- Topic: filterBam compiling error
- Replies: 11
- Views: 17365
Re: filterBam compiling error
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 -...
- Thu Nov 19, 2015 2:55 pm
- Forum: AUGUSTUS Compilation/Installation
- Topic: filterBam compiling error
- Replies: 11
- Views: 17365
Re: filterBam compiling error
by katharina on 20.07.2015 - 11:48
Then please remove the pre-compiled *.o files and try again.
Then please remove the pre-compiled *.o files and try again.
- Thu Nov 19, 2015 2:55 pm
- Forum: AUGUSTUS Compilation/Installation
- Topic: filterBam compiling error
- Replies: 11
- Views: 17365
Re: filterBam compiling error
by Willow on 20.07.2015 - 09:24
No,I did not remove any files of filterBam
No,I did not remove any files of filterBam
- Thu Nov 19, 2015 2:55 pm
- Forum: AUGUSTUS Compilation/Installation
- Topic: filterBam compiling error
- Replies: 11
- Views: 17365
Re: filterBam compiling error
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.
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.
- Thu Nov 19, 2015 2:55 pm
- Forum: AUGUSTUS Compilation/Installation
- Topic: filterBam compiling error
- Replies: 11
- Views: 17365
Re: filterBam compiling error
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...
- Thu Nov 19, 2015 2:55 pm
- Forum: AUGUSTUS Compilation/Installation
- Topic: filterBam compiling error
- Replies: 11
- Views: 17365
Re: filterBam compiling error
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
- Thu Nov 19, 2015 2:54 pm
- Forum: AUGUSTUS Compilation/Installation
- Topic: filterBam compiling error
- Replies: 11
- Views: 17365
Re: filterBam compiling error
Originally posted by Willow in the old forum on 01.07.2015 - 15:42
bamtools-2.4.0
bamtools-2.4.0
- Thu Nov 19, 2015 2:52 pm
- Forum: AUGUSTUS Compilation/Installation
- Topic: filterBam compiling error
- Replies: 11
- Views: 17365
Re: filterBam compiling error
Originally posted by Katharina in the old forum on 01.07.2015 - 11:56
Which version of bamtools did you use?
Which version of bamtools did you use?
- Thu Nov 19, 2015 2:51 pm
- Forum: AUGUSTUS Compilation/Installation
- Topic: filterBam compiling error
- Replies: 11
- Views: 17365
filterBam compiling error
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...
- Thu Nov 19, 2015 2:50 pm
- Forum: Training AUGUSTUS
- Topic: Error while running autoAug.pl
- Replies: 6
- Views: 6388
Re: Error while running autoAug.pl
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.
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.
- Thu Nov 19, 2015 2:49 pm
- Forum: Training AUGUSTUS
- Topic: Error while running autoAug.pl
- Replies: 6
- Views: 6388
Re: Error while running autoAug.pl
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...
- Thu Nov 19, 2015 2:49 pm
- Forum: Training AUGUSTUS
- Topic: Error while running autoAug.pl
- Replies: 6
- Views: 6388
Re: Error while running autoAug.pl
Originally posted by tnguyen in the old forum on 15.10.2012 - 14:48
Thank you Katharina.
T
Thank you Katharina.
T
- Thu Nov 19, 2015 2:48 pm
- Forum: Training AUGUSTUS
- Topic: Error while running autoAug.pl
- Replies: 6
- Views: 6388
Re: Error while running autoAug.pl
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...
- Thu Nov 19, 2015 2:48 pm
- Forum: Training AUGUSTUS
- Topic: Error while running autoAug.pl
- Replies: 6
- Views: 6388
Re: Error while running autoAug.pl
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:$PATH"
export PATH
and it is not working still.
Thank you Kathrina,
I did add the PATH as follows:
PATH="/group/aquaculture/mussels/sequencing/programs/Scipio/scipio-1.4:$PATH"
export PATH
and it is not working still.
- Thu Nov 19, 2015 2:47 pm
- Forum: Training AUGUSTUS
- Topic: Error while running autoAug.pl
- Replies: 6
- Views: 6388
Re: Error while running autoAug.pl
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 ....
- Thu Nov 19, 2015 2:47 pm
- Forum: Training AUGUSTUS
- Topic: Error while running autoAug.pl
- Replies: 6
- Views: 6388
Error while running autoAug.pl
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...