[maker-devel] maker dying on a contig

[Karyn Megy]

Hi Jeremy, 

Could it be a contig with lots of repeats, or that would hit lots of proteins?

One of my colleague had this issue and he ended splitting the few problematic contigs in sections... but then you have to reconciliate the results because the gene/BLAST coordinates are based in the bits of sub-contigs rather than the initial contig.  

You could try running MAKER on half of this contig and see what happen.

Cheers,
Karyn.

On 24 Aug 2012, at 08:44, Michael Thon wrote:

> I'm not sure if this is relevant to your problem but I had problems with maker failing on some contigs but not others.  I reinstalled maker and used the Build script to have it install all of its own dependencies.  Now maker is running fine, although the culprit seems to have been the blast version I was using before.
> 
> 
> On Aug 21, 2012, at 6:26 PM, Jeremy Semeiks <jeremy.semeiks at utsw.edu> wrote:
> 
>> Hi,
>> 
>> I'm trying to annotate a mammalian genome with maker-2.26-beta. I have
>> ~36,000 contigs, and per the master log maker FINISHED all of them
>> except one (scaffold_10105, ~60 kbp, not obviously weird) on the first
>> run. It didn't report ERROR for that contig in the master log, but it
>> did output two DIED lines in the contig's run.log and then just hung
>> for a week until I killed it.
>> 
>> I reran maker on just that contig by deleting the START line from the
>> master log. maker again died on that contig.
>> 
>> I attach the relevant part of the stderr stream; the rest was just
>> "--Next Contig--"-type lines. Any ideas?
>> 
>> A related question. Is deleting lines in the master log, as I did
>> here, the best way to get maker to rerun on just a few contigs? I
>> often find myself needing to do this, sometimes because of ERROR lines
>> or other assumed quirks in maker and sometimes just because I needed
>> to pause a big run for a while. One disadvantage is that when I
>> restart, maker needs to manually scan over many completed contigs,
>> which takes a while.
>> 
>> (I'd think the best solution would be for maker to automatically
>> recognize whether it's really currently running on contigs marked
>> STARTED but not FINISHED. It doesn't seem to do this now, but I
>> realize that might be hard to implement.)
>> 
>> Thanks,
>> Jeremy
>> Grad student, Grishin lab
>> UT Southwestern, Dallas TX
>> 510.384.8959
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> 
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