[maker-devel] query

Wed Dec 26 02:34:43 MST 2012

Thanks all.

The maker is now running properly. I don't know where the problem actually
was. I re install everything and now its working.

I'll let you know if there are any problems in future.

Thanks!

On Sat, Dec 22, 2012 at 12:44 AM, Carson Holt <carsonhh at gmail.com> wrote:

> 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=130da06dcd7f8e6a&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
>>>
>>>
>>>
>>>
>>>
>>
>>
>>
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>>
>>
>
>
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Indu
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