Search found 530 matches

by katharina
Thu Nov 19, 2015 2:56 pm
Forum: AUGUSTUS Compilation/Installation
Topic: filterBam compiling error
Replies: 11
Views: 5862

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...
by katharina
Thu Nov 19, 2015 2:56 pm
Forum: AUGUSTUS Compilation/Installation
Topic: filterBam compiling error
Replies: 11
Views: 5862

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...
by katharina
Thu Nov 19, 2015 2:56 pm
Forum: AUGUSTUS Compilation/Installation
Topic: filterBam compiling error
Replies: 11
Views: 5862

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!
by katharina
Thu Nov 19, 2015 2:56 pm
Forum: AUGUSTUS Compilation/Installation
Topic: filterBam compiling error
Replies: 11
Views: 5862

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 -...
by katharina
Thu Nov 19, 2015 2:55 pm
Forum: AUGUSTUS Compilation/Installation
Topic: filterBam compiling error
Replies: 11
Views: 5862

Re: filterBam compiling error

by katharina on 20.07.2015 - 11:48
Then please remove the pre-compiled *.o files and try again.
by katharina
Thu Nov 19, 2015 2:55 pm
Forum: AUGUSTUS Compilation/Installation
Topic: filterBam compiling error
Replies: 11
Views: 5862

Re: filterBam compiling error

by Willow on 20.07.2015 - 09:24
No,I did not remove any files of filterBam
by katharina
Thu Nov 19, 2015 2:55 pm
Forum: AUGUSTUS Compilation/Installation
Topic: filterBam compiling error
Replies: 11
Views: 5862

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.
by katharina
Thu Nov 19, 2015 2:55 pm
Forum: AUGUSTUS Compilation/Installation
Topic: filterBam compiling error
Replies: 11
Views: 5862

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...
by katharina
Thu Nov 19, 2015 2:55 pm
Forum: AUGUSTUS Compilation/Installation
Topic: filterBam compiling error
Replies: 11
Views: 5862

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
by katharina
Thu Nov 19, 2015 2:54 pm
Forum: AUGUSTUS Compilation/Installation
Topic: filterBam compiling error
Replies: 11
Views: 5862

Re: filterBam compiling error

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

bamtools-2.4.0
by katharina
Thu Nov 19, 2015 2:52 pm
Forum: AUGUSTUS Compilation/Installation
Topic: filterBam compiling error
Replies: 11
Views: 5862

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?
by katharina
Thu Nov 19, 2015 2:51 pm
Forum: AUGUSTUS Compilation/Installation
Topic: filterBam compiling error
Replies: 11
Views: 5862

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...
by katharina
Thu Nov 19, 2015 2:50 pm
Forum: Training AUGUSTUS
Topic: Error while running autoAug.pl
Replies: 6
Views: 3411

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.
by katharina
Thu Nov 19, 2015 2:49 pm
Forum: Training AUGUSTUS
Topic: Error while running autoAug.pl
Replies: 6
Views: 3411

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...
by katharina
Thu Nov 19, 2015 2:49 pm
Forum: Training AUGUSTUS
Topic: Error while running autoAug.pl
Replies: 6
Views: 3411

Re: Error while running autoAug.pl

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

Thank you Katharina.
T
by katharina
Thu Nov 19, 2015 2:48 pm
Forum: Training AUGUSTUS
Topic: Error while running autoAug.pl
Replies: 6
Views: 3411

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...
by katharina
Thu Nov 19, 2015 2:48 pm
Forum: Training AUGUSTUS
Topic: Error while running autoAug.pl
Replies: 6
Views: 3411

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.
by katharina
Thu Nov 19, 2015 2:47 pm
Forum: Training AUGUSTUS
Topic: Error while running autoAug.pl
Replies: 6
Views: 3411

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 ....
by katharina
Thu Nov 19, 2015 2:47 pm
Forum: Training AUGUSTUS
Topic: Error while running autoAug.pl
Replies: 6
Views: 3411

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...
by katharina
Thu Nov 19, 2015 2:46 pm
Forum: Training AUGUSTUS
Topic: UTR Training Question - copying the contents the utr.pbl file of another species
Replies: 1
Views: 1530

Re: UTR Training Question - copying the contents the utr.pbl file of another species

Originally posted by katharina in the old forum on 13.01.2015 - 04:22

You did the right thing.