[maker-devel] query

Fri Dec 21 10:40:10 MST 2012

In addition my last e-mailed explanation of eAED, here is where you can get
an explanation of how MAKER uses and calculates AED -->
http://www.biomedcentral.com/1471-2105/12/491
The original AED concept was borrowed from here  -->
http://www.biomedcentral.com/1471-2105/10/67

Thanks,
Carson

From:  Carson Holt <carsonhh at gmail.com>
Date:  Friday, 21 December, 2012 12:31 PM
To:  Daniel Ence <dence at genetics.utah.edu>, "maker-devel at yandell-lab.org"
<maker-devel at yandell-lab.org>
Subject:  Re: [maker-devel] query

Also try and capture the entire STDERR to a file for the failure, and attach
it to the e-mail.  The failure indicates that augustus itself failed.
Normally augustus should have provided it's own error message before the
"ERROR: Augustus failed" message.  If not it means that augusuts is failing
to even initialize.  If you send the whole STDERR we can find command line
MAKER used to run augustus, and we can let you try and execute the exact
same command line directly in a terminal (outside of MAKER) to see what
augustus does.

Thanks,
Carson

From:  Daniel Ence <dence at genetics.utah.edu>
Date:  Friday, 21 December, 2012 12:23 PM
To:  "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject:  Re: [maker-devel] query

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=130da06dcd7f8e6
>> a&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=130da06dcd7f8
e6a&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=130da06dcd7f8
e6a&attid=0.0.1&disp=emb&realattid=b8967bbd6e93d49d_0.25&zw> Indu Khatri
Institute of Microbial Technology,
Chandigarh-160036,
India

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