Search found 530 matches

by katharina
Thu Nov 19, 2015 2:45 pm
Forum: Training AUGUSTUS
Topic: UTR Training Question - copying the contents the utr.pbl file of another species
Replies: 1
Views: 1530

UTR Training Question - copying the contents the utr.pbl file of another species

Originally posted by Allison F in the old forum on 08.01.2015 - 21:09 I was able to train my gene model using the autoAug.pl script to generate the following files in my species gene model directory: My_fish_exon_probs.pbl My_fish_metapars.cfg My_fish_weightmatrix.txt My_fish_exon_probs.pbl.without...
by katharina
Thu Nov 19, 2015 2:43 pm
Forum: AUGUSTUS Compilation/Installation
Topic: bam2hints compiling error
Replies: 3
Views: 2926

Re: bam2hints compiling error

I don't think so. It is possible to extract CDS from the augustus output, afterwards, though.
by katharina
Thu Nov 19, 2015 2:43 pm
Forum: AUGUSTUS Compilation/Installation
Topic: bam2hints compiling error
Replies: 3
Views: 2926

Re: bam2hints compiling error

Originally posted by Willow in the old forum on 30.07.2015 - 09:41

Thank you very much!I have done my augustus process.I wonder if augustus can print the gff3 result and CDS separately into two files?
by katharina
Thu Nov 19, 2015 2:42 pm
Forum: AUGUSTUS Compilation/Installation
Topic: bam2hints compiling error
Replies: 3
Views: 2926

Re: bam2hints compiling error

Originally posted by katharina in the old forum on 22.07.2015 - 09:20

make clean deleted the *.o files.
Run "make" afterwards to compile bam2hints.
by katharina
Thu Nov 19, 2015 2:42 pm
Forum: AUGUSTUS Compilation/Installation
Topic: bam2hints compiling error
Replies: 3
Views: 2926

bam2hints compiling error

Originally posted by Willow on 21.07.2015 - 05:29 There are 4 files in the bam2hints directory: bam2hints.cc bam2hints.o Makefile README After I rewrote the absolute path of bamtools in Makefile,and type make clean,it returned rm -f bam2hints.o no executable was created while bam2hints.o removed
by katharina
Thu Nov 19, 2015 2:41 pm
Forum: Training AUGUSTUS
Topic: Problem with autoAug.pl : transition file not found ???
Replies: 2
Views: 2028

Re: Problem with autoAug.pl : transition file not found ???

You can set your customized AUGUSTUS_CONFIG_PATH variable that points to the location of your config files. Either set it in your .bashrc/.profile file, or add it as a command line argument to each augustus call.
by katharina
Thu Nov 19, 2015 2:40 pm
Forum: Training AUGUSTUS
Topic: Problem with autoAug.pl : transition file not found ???
Replies: 2
Views: 2028

Re: Problem with autoAug.pl : transition file not found ???

Originally posted by Marie in the old forum on 04.11.2014 - 16:37 Hey ! I found a way to fix this problem. From the beginning, the script looks for information in augustus/bin/model and augustus/bin/species rather than in augustus/config. So I copied myspecies/ and model/ directories from config to...
by katharina
Thu Nov 19, 2015 2:40 pm
Forum: Training AUGUSTUS
Topic: Problem with autoAug.pl : transition file not found ???
Replies: 2
Views: 2028

Problem with autoAug.pl : transition file not found ???

Originally posted by Marie in the old forum on 03.11.2014 - 16:22 Hello, I am using autoAug.pl to train Augustus on a new species. However, there is an error : augustus --species=myspecies /Data/Genomics/GeneAnnotation/Maker_pipeline/3_Train_Augustus/Using_M aker/Training2/autoAug/autoAugTrain/trai...
by katharina
Thu Nov 19, 2015 2:38 pm
Forum: Predicting Genes with AUGUSTUS
Topic: AUGUSTUS PPX memory problem
Replies: 1
Views: 1173

Re: AUGUSTUS PPX memory problem

Originally posted by Mario in the old forum on 05.12.2013 - 11:25 This is likely to result from cases where - due to repeats - the profile or some of the blocks generate an excessive number of hits. A proper fix will require some programming effort on our side. I suggest, you go for a quick fix: a)...
by katharina
Thu Nov 19, 2015 2:37 pm
Forum: Predicting Genes with AUGUSTUS
Topic: AUGUSTUS PPX memory problem
Replies: 1
Views: 1173

AUGUSTUS PPX memory problem

Originally posted by Luke in the old forum on 05.12.2013 - 11:20 I'm wondering if you can help me out with a weird memory problem I've run into run running augustus. It's the ppx extension. I'm looping over a batch of 1000 profiles, running a fastBlockSearch and then running augustus ppx on the bes...
by katharina
Thu Nov 19, 2015 2:36 pm
Forum: Training AUGUSTUS
Topic: new genome using augustus
Replies: 8
Views: 4088

Re: new genome using augustus

Originally posted by ipcc in the old forum on 06.08.2013 - 02:53

thank you , Mario.
by katharina
Thu Nov 19, 2015 2:36 pm
Forum: Training AUGUSTUS
Topic: new genome using augustus
Replies: 8
Views: 4088

Re: new genome using augustus

Originally posted by Mario in the old forum on 05.08.2013 - 08:44

The predictions you obtained are ab initio. Go on if you want the ones using evidence (hints).
by katharina
Thu Nov 19, 2015 2:35 pm
Forum: Training AUGUSTUS
Topic: new genome using augustus
Replies: 8
Views: 4088

Re: new genome using augustus

Originally posted by ipcc in the old forum on 05.08.2013 - 00:48 Hi, I got the out put like this: 1 ####### Finished step 1 at Fri Aug 2 15:42:31 2013. All files are stored in /diag/home/zjrouc/annotation/scalek58_augustus//autoAug/autoAugTrain ####### 1 ####### Step 2: Preparing scripts for AUGUST...
by katharina
Thu Nov 19, 2015 2:35 pm
Forum: Training AUGUSTUS
Topic: new genome using augustus
Replies: 8
Views: 4088

Re: new genome using augustus

Originally posted by katharina in the old forum on 29.07.2013 - 10:18

I think that could work. I haven't tried it, myself, though.
Katharina
by katharina
Thu Nov 19, 2015 2:34 pm
Forum: Training AUGUSTUS
Topic: new genome using augustus
Replies: 8
Views: 4088

Re: new genome using augustus

Originally posted by ipcc in the old forum on 26.07.2013 - 23:48 Dear Katharina, I've got the .gff file from CEGMA. So my command will be autoAug.pl --species=NewSpecies --genome=genome.fa --trainingset=augustus.gff Is this correct? I don't have any cDNA or Protein sequence of this species, is that...
by katharina
Thu Nov 19, 2015 2:27 pm
Forum: Training AUGUSTUS
Topic: new genome using augustus
Replies: 8
Views: 4088

Re: new genome using augustus

Originally posted by katharina in the old forum on 24.07.2013 - 09:17 It is a script that will create a folder with "untrained" config files for training a new species. If you use autoAug.pl, new_species.pl is automatically invoked. If you want to train a species "manually" (i.e...
by katharina
Thu Nov 19, 2015 2:27 pm
Forum: Training AUGUSTUS
Topic: new genome using augustus
Replies: 8
Views: 4088

Re: new genome using augustus

Originally posted by ipcc in the old forum on 23.07.2013 - 17:09

Dear Katharina,
How about new_species.pl? I found this in scripts/ folder, is that supposed to be an training script for new species?
by katharina
Thu Nov 19, 2015 2:26 pm
Forum: Training AUGUSTUS
Topic: new genome using augustus
Replies: 8
Views: 4088

Re: new genome using augustus

Originally posted by katharina in the old forum on 18.07.2013 - 15:53 It is not possible to train AUGUSTUS without a reliable set of training gene structures. If you lack experimental data of your target species, you might want to give CEGMA a try: http://bioinf.uni-greifswald.de/bioinf/wiki/pmwiki...
by katharina
Thu Nov 19, 2015 2:26 pm
Forum: Training AUGUSTUS
Topic: new genome using augustus
Replies: 8
Views: 4088

new genome using augustus

Originally posted by ipcc in the old forum on 18.07.2013 - 03:24 Hi, I am new using this software. Now i am trying to use AUGUSTUS to annotate a new genome sequence without training parameters. The problem is the software ask to train the genome using genome sequence and at least one following file...
by katharina
Thu Nov 19, 2015 2:25 pm
Forum: Predicting Genes with AUGUSTUS
Topic: rna-seq
Replies: 3
Views: 1871

Re: rna-seq

Originally posted by katharina in the old forum on 13.10.2013 - 18:14 You could try to split the larger genbank file into smaller files in order to find the location of the problem (it's likely caused by an incorrectly formatted entry). After identification, remove the error causing entry from the ...