[maker-devel] maker dying on a contig

[Jeremy Semeiks]

After doing this, I still get the same errors as I attached before.
There was also nothing in the log supporting that maker tried this
more than once. (Initially, I had tries=2, but I changed it to
tries=10 for this run. I'm guessing that's what you mean by "retry
count".) It also doesn't matter if I keep the same old contig
directory and master log before rerunning, or if I delete them both.

FWIW, maker's own version of blast is 2.2.26+, which is the same as my
native version.

Thanks,
Jeremy

On Fri, Aug 24, 2012 at 2:17 PM, Carson Holt <carsonhh at gmail.com> wrote:
> Let maker install it's own blast (a version I know should work).
>
> cd ./maker/src
> ./Build blast
>
> Then to finish up your job (this command will just update executable
> locations in the maker_exe.ctl file) -->
> maker -EXE
>
> Then run maker again with a higher retry count.  Let me know if the contig
> still fails.
>
> Thanks,
> Carson
>
>
>
>
> On 12-08-24 3:13 PM, "Jeremy Semeiks" <jeremy.semeiks at utsw.edu> wrote:
>
>>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
>>>>> <maker.stderr>_______________________________________________
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>>>>> maker-devel at box290.bluehost.com
>>>>>
>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>>
>>>>
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>>>
>>>
>
>