[maker-devel] Fwd: query

[indu khatri]

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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