Search found 531 matches

by katharina
Thu Nov 19, 2015 3:08 pm
Forum: Training AUGUSTUS
Topic: UTR annotation
Replies: 5
Views: 4901

Re: UTR annotation

by katharina on 06.09.2013 - 17:34
I would simpley remove the error-causing gebank entry (or have a close look at how it is different from other non-error causing entries).
Katharina
by katharina
Thu Nov 19, 2015 3:08 pm
Forum: Training AUGUSTUS
Topic: UTR annotation
Replies: 5
Views: 4901

Re: UTR annotation

by Sammy on 06.09.2013 - 17:22 Hi Katharina, I am running optimize_augustus.pl with --UTR=on --trainOnlyUtr=1 and other flags. I am getting long list of error as Encountered error after reading 505 annotations. Error: In sequence gnl|cnr_1.3|scaffold1852_175705-196609: One CDS exon begins before th...
by katharina
Thu Nov 19, 2015 3:07 pm
Forum: Training AUGUSTUS
Topic: UTR annotation
Replies: 5
Views: 4901

Re: UTR annotation

by katharina on 21.08.2013 - 15:40
This is not a problem. It is only a warning message. The input file apparently contained exon, CDS, and UTR feature annotation. But gff2gbSmalDNA.pl automatically extracts UTR features from the exon/CDS annotation.
Katharina
by katharina
Thu Nov 19, 2015 3:07 pm
Forum: Training AUGUSTUS
Topic: UTR annotation
Replies: 5
Views: 4901

UTR annotation

Originally posted in the old forum by Sammy on 20.08.2013 - 10:12 Hello all, I am using script gff2gbSmallDNA.pl to covert trainingSetComplete.gff into trainingSetComplete.gb. Here is the screen output Have mRNA and UTR for gene asmbl_9705 in sequence gnl|cnr_1.3|scaffold24. Ignoring UTR annotation...
by katharina
Thu Nov 19, 2015 3:05 pm
Forum: WebAUGUSTUS
Topic: WebAugustus alternative transcripts option -> which command line option?
Replies: 1
Views: 5185

Re: WebAugustus alternative transcripts option -> which command line option?

by katharina on 18.02.2015 - 11:44 none: --sample=100 --keep_viterbi=true --alternatives-from-sampling=false few: --sample=100 --keep_viterbi=true --alternatives-from-sampling=true --minexonintronprob=0.2 --minmeanexonintronprob=0.5 --maxtracks=2 medium: --sample=100 --keep_viterbi=true --alternati...
by katharina
Thu Nov 19, 2015 3:05 pm
Forum: WebAUGUSTUS
Topic: WebAugustus alternative transcripts option -> which command line option?
Replies: 1
Views: 5185

WebAugustus alternative transcripts option -> which command line option?

Originally posted in the old forum by Simon Perkins on 17.02.2015 - 16:22 Hello, We are running augustus locally as we have a big dataset to process, so we would like to map the web parameters we were going to use to command line parameters. Everything else can be set, but the "Alternative tra...
by katharina
Thu Nov 19, 2015 3:03 pm
Forum: AUGUSTUS Compilation/Installation
Topic: problem Install with Debian6
Replies: 1
Views: 5580

Re: problem Install with Debian6

by katharina on 24.09.2014 - 10:55 I believe you have to update your gclib (the package should be named libc6 on Debian). We haven't tested augustus on Debian, ourselves since all our machines run Ubuntu. Make sure that you compile augustus on the machine where you execute it. This is not an august...
by katharina
Thu Nov 19, 2015 3:03 pm
Forum: AUGUSTUS Compilation/Installation
Topic: problem Install with Debian6
Replies: 1
Views: 5580

problem Install with Debian6

Originally posted in the old forum by Cristina Frias on 22.09.2014 - 15:27 Hi, After Install we tried: root@hercules01:~# augustus --species=human --UTR=on /shared-soft/augustus-3.0.3/examples/example.fa augustus: /lib/libc.so.6: version `GLIBC_2.14' not found (required by augustus) augustus: /usr/...
by katharina
Thu Nov 19, 2015 3:02 pm
Forum: Training AUGUSTUS
Topic: Augustus 3.0 etraining input format error
Replies: 3
Views: 3715

Re: Augustus 3.0 etraining input format error

by Mario on 21.01.2014 - 12:15 I found the problem. It was with the function that determines the file type. Now all these combinations work: cd augustus/trunks/examples gzip -c hsackI10.gb > hsackI10.gb.gz gzip -c hsackI10.fa > hsackI10.fa.gz etraining --species=generic hsackI10.gb etraining --spec...
by katharina
Thu Nov 19, 2015 3:02 pm
Forum: Training AUGUSTUS
Topic: Augustus 3.0 etraining input format error
Replies: 3
Views: 3715

Re: Augustus 3.0 etraining input format error

by Malte Petersen on 21.01.2014 - 11:08 Thanks for your reply. I am not getting any error when using --species=human examples/HS08198.fa zlib and boost-iostreams are both installed (otherwise I could not have compiled the package). I should note that the leptopilina species is a custom config that ...
by katharina
Thu Nov 19, 2015 3:02 pm
Forum: Training AUGUSTUS
Topic: Augustus 3.0 etraining input format error
Replies: 3
Views: 3715

Re: Augustus 3.0 etraining input format error

by Mario on 21.01.2014 - 10:51 I am onto this. This problem is likely to be an effect of the new possibility to input gzipped input files with 3.0 (both genbank and fasta). Another user has reported this with augustus itself. However, we could not reproduce the error on our machines. It runs fine h...
by katharina
Thu Nov 19, 2015 3:02 pm
Forum: Training AUGUSTUS
Topic: Augustus 3.0 etraining input format error
Replies: 3
Views: 3715

Augustus 3.0 etraining input format error

Originally posted in the old forum by Malte Petersen on 13.01.2014 - 16:57 I am using the new Augustus version 3.0. It compiled fine and runs well, but if I want to retrain it, etraining complains about the input file not being in genbank format: ./bin/etraining --species=leptopilina /tmp/sequence....
by katharina
Thu Nov 19, 2015 3:01 pm
Forum: Training AUGUSTUS
Topic: improve existing AUGUSTUS parameters using RNA-Seq
Replies: 2
Views: 3134

Re: improve existing AUGUSTUS parameters using RNA-Seq

by katharina on 22.03.2012 - 16:19 In case the RNA-Seq assembly does not produce contigs of sufficient length, you could also use the following approach: 1) map the un-assembled RNA-Seq data against the existing transcript set 2) filter for transcripts that are fully covered by RNA-Seq data without...
by katharina
Thu Nov 19, 2015 3:00 pm
Forum: Training AUGUSTUS
Topic: improve existing AUGUSTUS parameters using RNA-Seq
Replies: 2
Views: 3134

Re: improve existing AUGUSTUS parameters using RNA-Seq

by Mario on 21.03.2012 - 14:31 those training sets came from Jason Stajich and I believe there were based on the CEGMA pipeline or some other protein homology method. Unfortunately, I can't find them anymore -- it is quite a long time ago. As you now have RNA-Seq, you can probably get better result...
by katharina
Thu Nov 19, 2015 3:00 pm
Forum: Training AUGUSTUS
Topic: improve existing AUGUSTUS parameters using RNA-Seq
Replies: 2
Views: 3134

improve existing AUGUSTUS parameters using RNA-Seq

The current, new answer to this topic is: Use BRAKER1! by Martin on 21.03.2012 - 14:23 I am using Augustus for gene predictions on Botrytis cinerea. I am wondering what training set was used to predict gene models using the species=botrytis_cinerea settings? I am involved in a Botrytis cinerea reseq...
by katharina
Thu Nov 19, 2015 2:59 pm
Forum: WebAUGUSTUS
Topic: formating the gff file
Replies: 5
Views: 9198

Re: formating the gff file

by Clement on 17.10.2014 - 13:08 Hey I think I just found the issue. It was really silly of me : after running the script for simplifying the headers of the genome file, the first column of the hint file was not corresponding to the genome file fasta headers anymore ...! Anyway it seems to be runni...
by katharina
Thu Nov 19, 2015 2:58 pm
Forum: WebAUGUSTUS
Topic: formating the gff file
Replies: 5
Views: 9198

Re: formating the gff file

by katharina on 17.10.2014 - 13:01 That's weird. I have submitted a job with your file format (corrected line 3, adapted to fasta names in one of my fasta files, made sure the contigs are long enough): NT_039169.8 exonerate CDS 345798 345888 1 - . transcript_id "1" NT_039169.8 exonerate C...
by katharina
Thu Nov 19, 2015 2:58 pm
Forum: WebAUGUSTUS
Topic: formating the gff file
Replies: 5
Views: 9198

Re: formating the gff file

by Clement on 17.10.2014 - 12:28
the third line of the file is formated just like the three others.
sorry about the bad copy/paste.
by katharina
Thu Nov 19, 2015 2:58 pm
Forum: WebAUGUSTUS
Topic: formating the gff file
Replies: 5
Views: 9198

Re: formating the gff file

by Clement on 17.10.2014 - 12:26 Thanks for the link. I think I've adopted the exact same formating now (see below) and still have the same error message... Any idea what else could be the problem ? Vielen dank! Clement pilon_round_18_contig_2558 exonerate CDS 345798 345888 1 - . transcript_id &quo...
by katharina
Thu Nov 19, 2015 2:58 pm
Forum: WebAUGUSTUS
Topic: formating the gff file
Replies: 5
Views: 9198

Re: formating the gff file

by katharina on 17.10.2014 - 07:58
You find a description of the accepted format at http://bioinf.uni-greifswald.de/webaugu ... ile_format
Have a look at the last column of your file.
Katharina