Search found 531 matches
- Tue Jul 25, 2017 8:55 am
- Forum: WebAUGUSTUS
- Topic: Local command line
- Replies: 1
- Views: 6585
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...
- Fri Mar 31, 2017 8:39 am
- Forum: Predicting Genes with AUGUSTUS
- Topic: protein hints - required scripts
- Replies: 1
- Views: 6370
Re: protein hints - required scripts
Hi Pedro,
I was on parental leave... I haven't finished going through my e-mails, yet. You will receive the script, eventually.
I am sorry that the person who was supposed to fill in for me in the forum did not do it...
Best,
Katharina
I was on parental leave... I haven't finished going through my e-mails, yet. You will receive the script, eventually.
I am sorry that the person who was supposed to fill in for me in the forum did not do it...
Best,
Katharina
- Fri Mar 31, 2017 8:38 am
- Forum: Predicting Genes with AUGUSTUS
- Topic: filterBAM error
- Replies: 1
- Views: 6742
Re: filterBAM error
Hi Francicco, I apologize for the long silence, I was on parental leave. If you are still having this problem, please send me a toy data set via e-mail and I will look into this. In general, I recommend you skip interative alignment. It is a procedure that we developed before today's RNA-Seq alignme...
- Fri Mar 31, 2017 8:34 am
- Forum: AUGUSTUS Compilation/Installation
- Topic: augustus PPX error (Mac Homebrew install)
- Replies: 2
- Views: 10753
Re: augustus PPX error (Mac Homebrew install)
I am sorry that we currently do not have the resources to fix bugs for Mac OS
We take this issue on our long list of bugs. Hopefully we will fix it one day.
I apologize for the long silence, I was on parental leave.
Best,
Katharina
We take this issue on our long list of bugs. Hopefully we will fix it one day.
I apologize for the long silence, I was on parental leave.
Best,
Katharina
- Fri Mar 31, 2017 8:33 am
- Forum: Training AUGUSTUS
- Topic: Error in etraining
- Replies: 1
- Views: 6946
Re: Error in etraining
Dear Ckuanglim, I assume that this is the complete error list, or that errors did not occur for ALL of the training gene structures that you had, i.e. most were ok. It happens that gene annotations are inconsistent. For example, sometimes, stop codons are annotated outside the CDS, even though they ...
- Fri Mar 31, 2017 8:29 am
- Forum: Training AUGUSTUS
- Topic: Error: Possibly "scipio" is not installed or not in your PATH
- Replies: 2
- Views: 7157
Re: Error: Possibly "scipio" is not installed or not in your PATH
Hi, I apologize that AutoAug.pl still produces this unspecific error message! (We will - hopefully - fix that one day...) The problem you are facing is that the output of scipio.pl $genome $trainingset > scipio.yaml 2> scipio.err does not contain what AutoAug.pl expects. Most often, this happens whe...
- Fri Mar 31, 2017 8:26 am
- Forum: Training AUGUSTUS
- Topic: GenBank format .gbff instead of .gb
- Replies: 1
- Views: 9998
Re: GenBank format .gbff instead of .gb
Hi Ferluz, gbff format itself should not be a problem, it is basically identical to gb format (two names for the same thing). However, AUGUSTUS is currently very strict when reading gb format. There can be many, many different issues. Please post an example of an entry that did not work for you, and...
- Fri Mar 31, 2017 8:22 am
- Forum: Training AUGUSTUS
- Topic: Corrupt Genbank format error
- Replies: 1
- Views: 6130
Re: Corrupt Genbank format error
Hi Sansan, I am apologize for not answering last year... I was on parental leave. Actually, somebody was supposed to answer questions here while I was gone, but he obviously didn't get around to do it... sorry. I cannot access the file, anymore. If you still have problems, please post a link to the ...
- Fri Mar 31, 2017 8:20 am
- Forum: Training AUGUSTUS
- Topic: optimize_augustus.pl results in lower prediction accuracy??
- Replies: 1
- Views: 6531
Re: optimize_augustus.pl results in lower prediction accuracy??
Hi Jon, thank you for pointing out that this can happen. I have also seen this in more than one genome annotation project. Always make a copy of original parameters before optimize_augustus.pl Always visualize prediction results in a browser with before/after optimize_augustus.pl Based on visualizat...
- Fri Mar 31, 2017 8:17 am
- Forum: Training AUGUSTUS
- Topic: Error when using filterBam on gsnap bam files
- Replies: 2
- Views: 7854
Re: Error when using filterBam on gsnap bam files
Hi Phil, I am not sure. I would need access to a toy data set of your bam file. It should not be a matter of /1 /2 read naming convention, anymore, since we fixed that issue a while ago. I am apologize for the long silence, I had been on parental leave. If you are still interested, please contact me...
- Mon Apr 18, 2016 9:26 am
- Forum: Predicting Genes with AUGUSTUS
- Topic: Extracting genes from newly sequenced data
- Replies: 3
- Views: 8375
Re: Extracting genes from newly sequenced data
There are no special flags involved. AUGUSTUS will not be aware of how well a certain parameter set "fits" to a particular genome.
I am currently not aware of a cichlid gene prediction project from our side.
I am currently not aware of a cichlid gene prediction project from our side.
- Tue Mar 29, 2016 6:22 pm
- Forum: Predicting Genes with AUGUSTUS
- Topic: Extracting genes from newly sequenced data
- Replies: 3
- Views: 8375
Re: Extracting genes from newly sequenced data
You have 2 options: 1) Use parameters of a related species for which AUGUSTUS has already been trained to predict genes in your novel sequences. Check which trained species is taxonomically closest to your species. 2) Train AUGUSTUS for your target species. This requires a high quality genome assemb...
- Fri Feb 05, 2016 12:58 pm
- Forum: WebAUGUSTUS
- Topic: quwstion about outfile
- Replies: 4
- Views: 9575
Re: quwstion about outfile
You are correct, simply grep lines that match \tAUGUSTUS\t.
Exception: if you ran AUGUSTUS with --gff3=on, then you will get a gff3 file, not a gtf file.
Exception: if you ran AUGUSTUS with --gff3=on, then you will get a gff3 file, not a gtf file.
- Wed Feb 03, 2016 4:02 pm
- Forum: BRAKER
- Topic: GeneMark: inappropriate ioctl for device
- Replies: 1
- Views: 7024
Re: GeneMark: inappropriate ioctl for device
Peter reported the following solution: Google serach: (http://stackoverflow.com/questions/1605195/inappropriate-ioctl-for-device) which identified this being this problem GLIBCXX_3.4.20 (http://www.unix.com/shell-programming-and-scripting/20812-inappropriate-ioctl-device.html) How to fix: http://ask...
- Wed Feb 03, 2016 4:02 pm
- Forum: BRAKER
- Topic: GeneMark: inappropriate ioctl for device
- Replies: 1
- Views: 7024
GeneMark: inappropriate ioctl for device
Peter reported to us:
As everything failed with GeneMark, I tried running this program alone:
gmes_petap.pl --ET hints.gff --sequence R.padi_final_genome.v1.fasta --et_score 10
The error came back as:
"inappropriate ioctl for device"
- Mon Dec 14, 2015 11:47 am
- Forum: Training AUGUSTUS
- Topic: One question about the using Scipio to do gene prediction
- Replies: 14
- Views: 21145
Re: One question about the using Scipio to do gene prediction
1. Predicted gene numbers of Scipio method (<5000) is much less than the protein numbers which I provided for training (~20000). More, this protein file was generated by transcriptome methods. I am not sure whether I understand. You say that you trained AUGUSTUS Scipio. Ok. And then you converted t...
- Tue Dec 01, 2015 1:20 pm
- Forum: Training AUGUSTUS
- Topic: One question about the using Scipio to do gene prediction
- Replies: 14
- Views: 21145
Re: One question about the using Scipio to do gene prediction
Yes, you found the right thing. But that is not a script to convert scipio training genes to hints, which is what you want to do. I recommend you script that, yourself. It should be very fast and easy, faster than running exonerate, in any case.
- Mon Nov 30, 2015 3:56 pm
- Forum: Predicting Genes with AUGUSTUS
- Topic: extract gene sequence from AUGUSTUS predictions
- Replies: 10
- Views: 21132
Re: extract gene sequence from AUGUSTUS predictions
getAnnoFasta.pl has two options to print coding sequences: 1) take the coding sequence from the AUGUSTUS output, directly. This is what happens in your case. The chop_cds flag is not applicable in that case. 2) extract coding sequence from genome file. This is required if the AUGUSTUS output does no...
- Mon Nov 30, 2015 2:31 pm
- Forum: Training AUGUSTUS
- Topic: One question about the using Scipio to do gene prediction
- Replies: 14
- Views: 21145
Re: One question about the using Scipio to do gene prediction
I don't think so. We have scripts to generate hints from proteins with exonerate (instead of scipio).Yafei wrote:Thanks again, BTW, are there some scripts for directly converting this scipio.gff file to hints file in the software scripts directory?
- Mon Nov 30, 2015 2:30 pm
- Forum: Training AUGUSTUS
- Topic: One question about the using Scipio to do gene prediction
- Replies: 14
- Views: 21145
Re: One question about the using Scipio to do gene prediction
It depends. source=P or src=P is the identifier for the scoring system to be used from extrinsic.cfg file for incorporating hints from type "P" (which is typically protein, yes). There are other possible flags to be added. Priority, e.g.: pri=3 If you have different sources of evidence wit...