[maker-devel] maker dying on a contig

[Carson Holt]

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
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>>>
>>>
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>>
>>