Search found 530 matches

by katharina
Fri Feb 01, 2019 10:34 am
Forum: WebAUGUSTUS
Topic: URL error - FASTA format
Replies: 4
Views: 6629

Re: URL error - FASTA format

The problem is that your file is sitting behind some kind of proxy or forwarding. WebAUGUSTUS can only access files that are directly available (i.e. resonse code 200, your file has resonse code 302).

If you consent, I can temporarily host the file on our server for you. Just let me know.

Katharina
by katharina
Sat Jun 23, 2018 4:39 pm
Forum: Training AUGUSTUS
Topic: Could not get same result with example data
Replies: 1
Views: 3469

Re: Could not get same result with example data

This is most commonly observed if the option --stopCodonExcludedFromCDS is set incorrectly (possibly, it has changed in the released parameters since the tutorial was created). Re-run AUGUSTUS with --stopCodonExcludedFromCDS=true (or false, depending on the current setting in your bug/bug_parameters...
by katharina
Mon Jun 11, 2018 10:19 am
Forum: Welcome to AUGUSTUS Forum!
Topic: Imprint/Data Privacy Protection
Replies: 0
Views: 6078

Imprint/Data Privacy Protection

We refer you to our imprint at http://bioinf.uni-greifswald.de/bioinf/impressum.html at to our data privacy protection declaration at http://bioinf.uni-greifswald.de/bioinf/datenschutz.html
by katharina
Tue May 08, 2018 1:14 pm
Forum: BRAKER
Topic: Braker using long evolutionary distant protein hints
Replies: 1
Views: 2328

Re: Braker using long evolutionary distant protein hints

Please contact Alexandre Lomsadze (or me) via e-mail.
by katharina
Thu Apr 12, 2018 8:56 am
Forum: Predicting Genes with AUGUSTUS
Topic: AUGUSTUS 3.3 hanging on contig
Replies: 2
Views: 2660

Re: AUGUSTUS 3.3 hanging on contig

I have notified Mario of this bug report. It might take a while to fix it, though.

Best,

Katharina
by katharina
Mon Apr 09, 2018 1:25 pm
Forum: Training AUGUSTUS
Topic: Training augustus with busco or?
Replies: 1
Views: 3133

Re: Training augustus with busco or?

I think what BUSCO does is use some existing AUGUSTUS species (custom defined or automatically chosen based on the selected database) to predict genes with PPX and retrain AUGUSTUS on the predictions (and then run another prediction iteration with PPX). The success of such an approach depends on how...
by katharina
Mon Apr 09, 2018 1:12 pm
Forum: Training AUGUSTUS
Topic: Training based on an existing profile
Replies: 1
Views: 2079

Re: Training based on an existing profile

Hi,

the human parameter set will most likely work very well for all mammalian species.

There was nothing wrong with your approach, it simplyl didn't lead to better results (and I wouldn't have expected it to).

Stick with human for mammalian genomes.

Best,

Katharina
by katharina
Mon Jan 29, 2018 9:15 am
Forum: BRAKER
Topic: failed executing genemark
Replies: 1
Views: 2974

Re: failed executing genemark

For issues that reproducibly exist with running GeneMark outside of BRAKER, please contact the GeneMark team (http://exon.gatech.edu/GeneMark/), directly.
by katharina
Mon Jan 29, 2018 9:12 am
Forum: Predicting Genes with AUGUSTUS
Topic: augustus - aborted (core dumped)
Replies: 1
Views: 2694

Re: augustus - aborted (core dumped)

Maybe it has happened, before. The best thing in such cases is to try to narrow down the problem to a tiny example to give us something to work with. E.g. try to reproduce the error on a single scaffold with a small hints file and a particular extrinsic.cfg file, a particular species parameter set.....
by katharina
Mon Jan 29, 2018 9:08 am
Forum: Predicting Genes with AUGUSTUS
Topic: Augustus PPX: Invalid block no. in SubstateModel::blockNoOfB
Replies: 2
Views: 28725

Re: Augustus PPX: Invalid block no. in SubstateModel::blockNoOfB

No, Mario had no time to look into this, yet. Sorry.
by katharina
Mon Jan 29, 2018 9:07 am
Forum: Predicting Genes with AUGUSTUS
Topic: bam2hints created an empty gff file
Replies: 1
Views: 2376

Re: bam2hints created an empty gff file

Is it possible that you maxed the memory of your computer? If the bam file is huge, this might happen.
by katharina
Mon Jan 29, 2018 9:07 am
Forum: Predicting Genes with AUGUSTUS
Topic: Augustus 3.3 stuck run
Replies: 1
Views: 2234

Re: Augustus 3.3 stuck run

Hi Mathieu, this is an issue that Mario accidentally put into the latest AUGUSTUS release. It has actually been fixed (internally). Please contact me via e-mail in case you need the fixed version. It is not a functional issue, though. It just causes a big output to stderr. katharina dot hoff at uni-...
by katharina
Thu Nov 09, 2017 3:41 pm
Forum: Training AUGUSTUS
Topic: UTR training error?
Replies: 4
Views: 4001

Re: UTR training error?

Yes, we haven't made a new AUGUSTUS release. It is already in function on WebAUGUSTUS.

If you send me an e-mail, I will send you the modified code. I am not sure how long it will take until we make a new AUGUSTUS release.

webaugustus@uni-greifswald.de
by katharina
Tue Oct 24, 2017 12:53 pm
Forum: Training AUGUSTUS
Topic: pre-compiled datasets
Replies: 2
Views: 2411

Re: pre-compiled datasets

Actually, there is no "one answer for all species". Training gene generation and selection was done in different ways for many species. Training genes are usually from the target organism. For older parameter sets, ESTs were often used as a basis, yes. For some species, protein sequences w...
by katharina
Tue Oct 24, 2017 12:50 pm
Forum: Training AUGUSTUS
Topic: UTR training error?
Replies: 4
Views: 4001

Re: UTR training error?

Thanks a lot for spotting and fixing this issue! Very nice of you to share! I have modified our codebase accordingly, WebAUGUSTUS is updated. The next source code release will also contain the fix.

The sampling error is unrelated. We are aware of it but it has not been fixed, yet.

Katharina
by katharina
Tue Oct 24, 2017 12:40 pm
Forum: WebAUGUSTUS
Topic: Password ?
Replies: 2
Views: 2769

Re: Password ?

The web service is password protected only for the temporary time when we need to reboot the machine but there are still running jobs that need to finish. The service will be available after reboot without password.
by katharina
Tue Jul 25, 2017 9:00 am
Forum: BRAKER
Topic: exonerate Protein alignments in Braker1
Replies: 1
Views: 3144

Re: exonerate Protein alignments in Braker1

It is currently not possible to use protein alignments with BRAKER1, yet. We are working on a new release that will enable you to do exactly this, but it is not out, yet.
by katharina
Tue Jul 25, 2017 9:00 am
Forum: BRAKER
Topic: Using braker for small open reading frame prediction
Replies: 1
Views: 2425

Re: Using braker for small open reading frame prediction

AUGUSTUS can in principle find small open reading frames. It is not an easy task, though. There is a parameter /Constant/min_coding_len that you can set to a shorter length (default is 201). You find that parameter in the species_parameters.cfg file for your species. However, this will probably not ...
by katharina
Tue Jul 25, 2017 8:59 am
Forum: BRAKER
Topic: Issue with BRAKER and AUGUSTUS
Replies: 2
Views: 3525

Re: Issue with BRAKER and AUGUSTUS

Hi Ying,

the current BRAKER release does not have this problem, anymore. It now works to specify a non-root AUGUSTUS_CONFIG_PATH.
by katharina
Tue Jul 25, 2017 8:55 am
Forum: WebAUGUSTUS
Topic: Local command line
Replies: 1
Views: 2210

Re: Local command line

The tool behind WebAUGUSTUS is autoAug.pl. You find it - including the command line if you call it with --help parameter, at http://bioinf.uni-greifswald.de/augustus/binaries/augustus.current.tar.gz in the scripts folder. Required software - besides AUGUSTUS - are PASA and Scipio. Please read the in...