Search found 531 matches
- Mon Feb 21, 2022 10:46 am
- Forum: Predicting Genes with AUGUSTUS
- Topic: Gene prediction with UTR=on option
- Replies: 1
- Views: 8797
Re: Gene prediction with UTR=on option
Fully automated UTR training of AUGUSTUS sometimes works great, and sometimes produces really poor results, as in your case. To date, I have no automated way to "know" beforehand. In some cases, the problem can be improved upon by setting the /UtrModel/polyasig_consensus in ${species}_para...
- Fri Feb 01, 2019 10:34 am
- Forum: WebAUGUSTUS
- Topic: URL error - FASTA format
- Replies: 4
- Views: 21875
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
If you consent, I can temporarily host the file on our server for you. Just let me know.
Katharina
- Sat Jun 23, 2018 4:39 pm
- Forum: Training AUGUSTUS
- Topic: Could not get same result with example data
- Replies: 1
- Views: 12317
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...
- Mon Jun 11, 2018 10:19 am
- Forum: Welcome to AUGUSTUS Forum!
- Topic: Imprint/Data Privacy Protection
- Replies: 0
- Views: 45773
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
- Tue May 08, 2018 1:14 pm
- Forum: BRAKER
- Topic: Braker using long evolutionary distant protein hints
- Replies: 1
- Views: 11219
Re: Braker using long evolutionary distant protein hints
Please contact Alexandre Lomsadze (or me) via e-mail.
- Thu Apr 12, 2018 8:56 am
- Forum: Predicting Genes with AUGUSTUS
- Topic: AUGUSTUS 3.3 hanging on contig
- Replies: 2
- Views: 12137
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
Best,
Katharina
- Mon Apr 09, 2018 1:25 pm
- Forum: Training AUGUSTUS
- Topic: Training augustus with busco or?
- Replies: 1
- Views: 12391
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...
- Mon Apr 09, 2018 1:12 pm
- Forum: Training AUGUSTUS
- Topic: Training based on an existing profile
- Replies: 1
- Views: 14517
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
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
- Mon Jan 29, 2018 9:15 am
- Forum: BRAKER
- Topic: failed executing genemark
- Replies: 1
- Views: 12145
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.
- Mon Jan 29, 2018 9:12 am
- Forum: Predicting Genes with AUGUSTUS
- Topic: augustus - aborted (core dumped)
- Replies: 1
- Views: 11423
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.....
- Mon Jan 29, 2018 9:08 am
- Forum: Predicting Genes with AUGUSTUS
- Topic: Augustus PPX: Invalid block no. in SubstateModel::blockNoOfB
- Replies: 2
- Views: 38105
Re: Augustus PPX: Invalid block no. in SubstateModel::blockNoOfB
No, Mario had no time to look into this, yet. Sorry.
- Mon Jan 29, 2018 9:07 am
- Forum: Predicting Genes with AUGUSTUS
- Topic: bam2hints created an empty gff file
- Replies: 1
- Views: 11118
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.
- Mon Jan 29, 2018 9:07 am
- Forum: Predicting Genes with AUGUSTUS
- Topic: Augustus 3.3 stuck run
- Replies: 1
- Views: 10910
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-...
- Thu Nov 09, 2017 3:41 pm
- Forum: Training AUGUSTUS
- Topic: UTR training error?
- Replies: 4
- Views: 22665
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
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
- Tue Oct 24, 2017 12:53 pm
- Forum: Training AUGUSTUS
- Topic: pre-compiled datasets
- Replies: 2
- Views: 13409
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...
- Tue Oct 24, 2017 12:50 pm
- Forum: Training AUGUSTUS
- Topic: UTR training error?
- Replies: 4
- Views: 22665
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
The sampling error is unrelated. We are aware of it but it has not been fixed, yet.
Katharina
- Tue Oct 24, 2017 12:40 pm
- Forum: WebAUGUSTUS
- Topic: Password ?
- Replies: 2
- Views: 12200
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.
- Tue Jul 25, 2017 9:00 am
- Forum: BRAKER
- Topic: exonerate Protein alignments in Braker1
- Replies: 1
- Views: 12122
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.
- Tue Jul 25, 2017 9:00 am
- Forum: BRAKER
- Topic: Using braker for small open reading frame prediction
- Replies: 1
- Views: 11381
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 ...
- Tue Jul 25, 2017 8:59 am
- Forum: BRAKER
- Topic: Issue with BRAKER and AUGUSTUS
- Replies: 2
- Views: 13340
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.
the current BRAKER release does not have this problem, anymore. It now works to specify a non-root AUGUSTUS_CONFIG_PATH.