Search found 530 matches

by katharina
Fri Mar 31, 2017 8:39 am
Forum: Predicting Genes with AUGUSTUS
Topic: protein hints - required scripts
Replies: 1
Views: 2011

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
by katharina
Fri Mar 31, 2017 8:38 am
Forum: Predicting Genes with AUGUSTUS
Topic: filterBAM error
Replies: 1
Views: 2353

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...
by katharina
Fri Mar 31, 2017 8:34 am
Forum: AUGUSTUS Compilation/Installation
Topic: augustus PPX error (Mac Homebrew install)
Replies: 2
Views: 5676

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
by katharina
Fri Mar 31, 2017 8:33 am
Forum: Training AUGUSTUS
Topic: Error in etraining
Replies: 1
Views: 2576

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 ...
by katharina
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: 2613

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...
by katharina
Fri Mar 31, 2017 8:26 am
Forum: Training AUGUSTUS
Topic: GenBank format .gbff instead of .gb
Replies: 1
Views: 3992

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...
by katharina
Fri Mar 31, 2017 8:22 am
Forum: Training AUGUSTUS
Topic: Corrupt Genbank format error
Replies: 1
Views: 2094

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 ...
by katharina
Fri Mar 31, 2017 8:20 am
Forum: Training AUGUSTUS
Topic: optimize_augustus.pl results in lower prediction accuracy??
Replies: 1
Views: 2307

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...
by katharina
Fri Mar 31, 2017 8:17 am
Forum: Training AUGUSTUS
Topic: Error when using filterBam on gsnap bam files
Replies: 2
Views: 3033

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...
by katharina
Mon Apr 18, 2016 9:26 am
Forum: Predicting Genes with AUGUSTUS
Topic: Extracting genes from newly sequenced data
Replies: 3
Views: 3049

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.
by katharina
Tue Mar 29, 2016 6:22 pm
Forum: Predicting Genes with AUGUSTUS
Topic: Extracting genes from newly sequenced data
Replies: 3
Views: 3049

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...
by katharina
Fri Feb 05, 2016 12:58 pm
Forum: WebAUGUSTUS
Topic: quwstion about outfile
Replies: 4
Views: 3852

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.
by katharina
Wed Feb 03, 2016 4:02 pm
Forum: BRAKER
Topic: GeneMark: inappropriate ioctl for device
Replies: 1
Views: 2562

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...
by katharina
Wed Feb 03, 2016 4:02 pm
Forum: BRAKER
Topic: GeneMark: inappropriate ioctl for device
Replies: 1
Views: 2562

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"
by katharina
Mon Dec 14, 2015 11:47 am
Forum: Training AUGUSTUS
Topic: One question about the using Scipio to do gene prediction
Replies: 14
Views: 8152

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...
by katharina
Tue Dec 01, 2015 1:20 pm
Forum: Training AUGUSTUS
Topic: One question about the using Scipio to do gene prediction
Replies: 14
Views: 8152

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.
by katharina
Mon Nov 30, 2015 3:56 pm
Forum: Predicting Genes with AUGUSTUS
Topic: extract gene sequence from AUGUSTUS predictions
Replies: 10
Views: 8279

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...
by katharina
Mon Nov 30, 2015 2:31 pm
Forum: Training AUGUSTUS
Topic: One question about the using Scipio to do gene prediction
Replies: 14
Views: 8152

Re: One question about the using Scipio to do gene prediction

Yafei wrote:Thanks again, BTW, are there some scripts for directly converting this scipio.gff file to hints file in the software scripts directory?
I don't think so. We have scripts to generate hints from proteins with exonerate (instead of scipio).
by katharina
Mon Nov 30, 2015 2:30 pm
Forum: Training AUGUSTUS
Topic: One question about the using Scipio to do gene prediction
Replies: 14
Views: 8152

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...
by katharina
Mon Nov 30, 2015 12:46 pm
Forum: Training AUGUSTUS
Topic: One question about the using Scipio to do gene prediction
Replies: 14
Views: 8152

Re: One question about the using Scipio to do gene prediction

If available, I add the evidence, sure.

Maybe you should run both. You need to examine results in a Browser, anyway, and then you can compare: scipio genes, ab initio predictions and predictions with scipio hints.