[maker-devel] query

Fri Dec 21 12:07:40 MST 2012

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<mailto: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<mailto:indu2287 at gmail.com>]
Sent: Thursday, December 20, 2012 12:41 PM
To: maker-devel at yandell-lab.org<mailto: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<mailto: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

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Barry Moore
Research Scientist
Dept. of Human Genetics
University of Utah
Salt Lake City, UT 84112
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(801) 585-3543

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Institute of Microbial Technology,
Chandigarh-160036,
India

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Institute of Microbial Technology,
Chandigarh-160036,
India

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PhD Research Fellow,
C/o Dr. Srikrishna Subramanian
Institute of Microbial Technology,
Chandigarh-160036,
India

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