[maker-devel] query

Fri Dec 21 10:58:31 MST 2012

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
>>
>>
>>
>>
>>
>
>
>  --
> <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
>
>
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-- 
<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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