[maker-devel] query

[Barry Moore]

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
> 
> -- 
> 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
--------------------------------------------
(801) 585-3543




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