[maker-devel] maker dying on a contig

[Carson Holt]

Could you send the blast version informations for reference purposes? I
can see this being caused by BLAST.

Thanks,
Carson



On 12-08-24 3:44 AM, "Michael Thon" <mike.thon at gmail.com> 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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