[maker-devel] query

Fri Dec 21 12:14:38 MST 2012

Daniel is right. If it's another Fusarium species retraining probably isn't
necessary (distantly related fungi would probably need retraining though).
I'd recommend using GeneMark as well though.  It is very easy to train and
works well on Fungi species.  Could you include the version of Augustus you
are using and the sequence for the contig that fails when you send the
STDERR.

Thanks,
Carson

From:  Daniel Ence <dence at genetics.utah.edu>
Date:  Friday, 21 December, 2012 2:07 PM
To:  "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject:  Re: [maker-devel] query

Hi Indu, Can you send the error output that Carson mentioned? Using a
closely related augustus model for your organism can be a good approach, if
that's the best you can do. Training augustus for your organism would be
better, but you don't have to do it.

Thanks,
Daniel

Daniel Ence
Graduate Student
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330

From: indu khatri [indu2287 at gmail.com]
Sent: Friday, December 21, 2012 10:58 AM
To: Daniel Ence
Cc: maker-devel at yandell-lab.org
Subject: Re: [maker-devel] query

Hii Daniel 

It was failing for 1 contig only. The contig length is approx 1.5 Mb.
Excluding that contig the run was successful. I am using RepeatMasker
libraries only for masking the sequences. I used Fusarium graminearum
species as Augustus model species.

I have one more query about Maker annotation results. Only augustus as gene
predictor can be a good predictor for annotations or I have to retrain it
using the previous results from first runs of MAKER in order to get
validated gene models.

Thanks.

On Fri, Dec 21, 2012 at 9:23 AM, Daniel Ence <dence at genetics.utah.edu>
wrote:
> Hi Indu, 
> 
> I'm going to echo Barry's request for more details about this problem too.
> Does augustus fail on more than one contig or does it fail repeatedly on the
> same contig? If its only contig, how big is that contig and is it possibly all
> masked out by repeatmasker? If you exclude that one contig, do the rest run
> successfully?  What are you using to mask the repeats in the genome? Which
> augustus model are you using, and how did you choose that model?
> 
> Thanks,
> Daniel
> 
> Daniel Ence
> Graduate Student
> Eccles Institute of Human Genetics
> University of Utah
> 
> 15 North 2030 East, Room 2100
> Salt Lake City, UT 84112-5330
> 
> From: indu khatri [indu2287 at gmail.com]
> Sent: Thursday, December 20, 2012 12:41 PM
> To: maker-devel at yandell-lab.org
> Cc: Barry Moore; Daniel Ence
> Subject: Fwd: [maker-devel] query
> 
> 
> Thanks Daniel and Barry for your reply.
> 
> I have sorted out that problem. It was due to very distant homolog species I
> chose for training.
> 
> But, I am still getting some errors while running MAKER.
> ERROR: Augustus failed
> ERROR: Failed while preparing ab-inits
> ERROR: Chunk failed at level:4, tier_type:0
> FAILED CONTIG
> 
> Can you please tell me what is the possible reason for this error?
> 
> Thanks in advance.
> 
> 
> 
> On Thu, Dec 20, 2012 at 10:50 PM, Barry Moore <barry.moore at genetics.utah.edu>
> wrote:
>> Hi Indu, 
>> 
>> The error output as Daniel suggested would be great and also a bit more
>> detail on the problem.  Is it stalled on a long contig - how long?  How long
>> has it been stalled for?  How many cpus are you running?  Are you running
>> under MPI?  How big is the protein evidence file?  If you're using the altest
>> function for your ESTs then it's running tblastx which is up to 10X slower
>> than blastn with regular ESTs, is it possible that you're stuck on tblastx?
>> 
>> Finally, it can help if you isolate the problem a bit.  Can you run
>> successfully on any of your contigs by running single contigs in your fasta
>> file?  If it's stalled on a large contig, iteratively cut it in half and see
>> if the problem isolates to one part of the contig.
>> 
>> B
>> 
>> On Dec 19, 2012, at 10:33 PM, indu khatri wrote:
>> 
>>>  Hello Maker-devel
>>>     Thanks for adding me to the list. I am new to this field. I have a query
>>> regarding maker annotation.
>>>     I have assembled a fungal Genome with 1590 contigs and was trying to
>>>     annotate it using MAKER pipeline. I only have paired end WGS sequence
>>> from
>>>     Illumina HiSeq sequencing which were assembled using CLCbio. I dont have
>>>     any transcriptome data. I am using ESTs of a closer species for
>>> validation
>>>     and similarly the protein sequences. I have started annotation but the
>>>     problem is the pipeline gets stuck to the first contig on blastx step
>>> and
>>>     doesn't move further. I could not make out the problem. Can you please
>>> help
>>>     me out of this.
>>> 
>>> Thanks and regards
>>> 
>>> -- 
>>>  
>>> <https://mail.google.com/mail/?ui=2&ik=8ec2492227&view=att&th=130da06dcd7f8e
>>> 6a&attid=0.0.1&disp=emb&realattid=b8967bbd6e93d49d_0.25&zw> Indu Khatri
>>> PhD Research Fellow,
>>> C/o Dr. Srikrishna Subramanian
>>> Institute of Microbial Technology,
>>> Chandigarh-160036,
>>> India
>>> 
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>> 
>> Barry Moore
>> Research Scientist
>> Dept. of Human Genetics
>> University of Utah
>> Salt Lake City, UT 84112
>> --------------------------------------------
>> (801) 585-3543
>> 
>> 
>> 
>> 
> 
> 
> 
> -- 
>  
> <https://mail.google.com/mail/?ui=2&ik=8ec2492227&view=att&th=130da06dcd7f8e6a
> &attid=0.0.1&disp=emb&realattid=b8967bbd6e93d49d_0.25&zw> Indu Khatri
> Institute of Microbial Technology,
> Chandigarh-160036,
> India
> 
> 
> 
> 
> -- 
>  
> <https://mail.google.com/mail/?ui=2&ik=8ec2492227&view=att&th=130da06dcd7f8e6a
> &attid=0.0.1&disp=emb&realattid=b8967bbd6e93d49d_0.25&zw> Indu Khatri
> Institute of Microbial Technology,
> Chandigarh-160036,
> India
> 
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> 

-- 
 <https://mail.google.com/mail/?ui=2&ik=8ec2492227&view=att&th=130da06dcd7f8
e6a&attid=0.0.1&disp=emb&realattid=b8967bbd6e93d49d_0.25&zw> Indu Khatri
PhD Research Fellow,
C/o Dr. Srikrishna Subramanian
Institute of Microbial Technology,
Chandigarh-160036,
India

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