[maker-devel] maker dying on a contig

[Jeremy Semeiks]

Carson,

$ blastx -version
blastx: 2.2.26+
Package: blast 2.2.26, build Feb 22 2012 16:04:28

- J

On Fri, Aug 24, 2012 at 7:24 AM, Carson Holt <carsonhh at gmail.com> wrote:
> 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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>>
>>
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>
>