[maker-devel] Failed while polishing ESTs

[Seth Munholland]

I'll wipe it clean and do a fresh install of everything to be 100% safe.

Seth Munholland, B.Sc.
Department of Biological Sciences
Rm. 304 Biology Building
University of Windsor
401 Sunset Ave. N9B 3P4
T: (519) 253-3000 Ext: 4755

On Wed, Feb 22, 2017 at 2:03 PM, Carson Holt <carsonhh at gmail.com> wrote:

> I still think you may have something wrong somewhere with some part of
> your installation (rogue libraries, compiler incompatibilities, etc.).
> Especially given your earlier issues with Perl libraries.
>
> —Carson
>
>
> On Feb 22, 2017, at 12:00 PM, Seth Munholland <munholl at uwindsor.ca> wrote:
>
> On a whim I decided to switch to the hsap demo data and it completed
> without issue.  I went back to dpp and this time is completed.  I hadn't
> changed anything but the maker_opts.ctl lines that had "dpp" to "hsap" and
> then inverted the change.
>
> Mayhaps there was something not unloaded from memory in an earlier run?
> It's that, ghosts, or rogue ions :/
>
> Seth Munholland, B.Sc.
> Department of Biological Sciences
> Rm. 304 Biology Building
> University of Windsor
> 401 Sunset Ave. N9B 3P4
> T: (519) 253-3000 Ext: 4755
>
> On Wed, Feb 22, 2017 at 1:57 PM, Seth Munholland <munholl at uwindsor.ca>
> wrote:
>
>> It is the test data, the dpp set to be specific.
>>
>> I already checked all the installs to be sure they configured and compile
>> without error and are up to date.
>>
>> I've been deleting between each run.
>>
>> Seth Munholland, B.Sc.
>> Department of Biological Sciences
>> Rm. 304 Biology Building
>> University of Windsor
>> 401 Sunset Ave. N9B 3P4
>> T: (519) 253-3000 Ext: 4755
>>
>> On Wed, Feb 22, 2017 at 1:16 PM, Carson Holt <carsonhh at gmail.com> wrote:
>>
>>> So you are running the test data job correct? So if you get any error
>>> with the test data job, something is wrong with your installation.
>>>
>>> Make sure BioPerl is up to data (and the same everywhere). If using your
>>> own installation of Perl, make sure it had BerkleyDB support when you
>>> installed it (if you are using something like perlbrew , you may not have
>>> BerkleyDB support and this may affect BioPerl indexing). Also try
>>> reinstalling exonertate.
>>>
>>> And make sure to delete any run directories before retrying.
>>>
>>> —Carson
>>>
>>>
>>> On Feb 22, 2017, at 11:03 AM, Seth Munholland <munholl at uwindsor.ca>
>>> wrote:
>>>
>>> After my clustering issue I figured I would go node by node and run
>>> MAKER locally on the test data set to be sure that it was working properly
>>> before trying it as a full MPI run.  After adjusting all my exes to point
>>> to the NFS versions I am consistently getting the same error on each node
>>> when it comes time to run exonerate:
>>>
>>> polishig ESTs
>>> running  est2genome search.
>>> #--------- command -------------#
>>> Widget::exonerate::est2genome:
>>> /Data/Apps/exonerate/src/program/exonerate  -q
>>> /tmp/maker_q3n9fB/0/dpp-mRNA-5.for.26386-32056.0.fasta -t
>>> /tmp/maker_q3n9fB/0/contig-dpp-500-500.26386-32056.0.fasta -Q dna -T
>>> dna --model est2genome  --minintron 20 --maxintron 10000 --showcigar
>>> --percent 20 > /tmp/maker_q3n9fB/0/contig-dpp
>>> -500-500.26386-32056.dpp-mRNA-5.e.exonerate
>>> #-------------------------------#
>>> Messed up acceptor:TT in Widget::exonerate::est2genome::get_acceptor!
>>> --> rank=NA, hostname=beanblade2
>>> ERROR: Failed while polishig ESTs
>>> ERROR: Chunk failed at level:2, tier_type:3
>>> FAILED CONTIG:contig-dpp-500-500
>>>
>>> ERROR: Chunk failed at level:4, tier_type:0
>>> FAILED CONTIG:contig-dpp-500-500
>>>
>>> The only results I find on google was an issue with an improper
>>> character in the est file, but a cat of the dpp_est.fasta shows nothing
>>> incorrect and since they all point to dpp-mRNA-5 I backed up the provided
>>> est and removed it.  The response was:
>>>
>>> polishig ESTs
>>> running  est2genome search.
>>> #--------- command -------------#
>>> Widget::exonerate::est2genome:
>>> /Data/Apps/exonerate/src/program/exonerate  -q
>>> /tmp/maker_I7TZxt/0/dpp-mRNA-4.for.22889-32056.0.fasta -t
>>> /tmp/maker_I7TZxt/0/contig-dpp-500-500.22889-32056.0.fasta -Q dna -T
>>> dna --model est2genome  --minintron 20 --maxintron 10000 --showcigar
>>> --percent 20 > /tmp/maker_I7TZxt/0/contig-dpp
>>> -500-500.22889-32056.dpp-mRNA-4.e.exonerate
>>> #-------------------------------#
>>> Messed up acceptor:TT in Widget::exonerate::est2genome::get_acceptor!
>>> --> rank=NA, hostname=beanblade4
>>> ERROR: Failed while polishig ESTs
>>> ERROR: Chunk failed at level:2, tier_type:3
>>> FAILED CONTIG:contig-dpp-500-500
>>>
>>> ERROR: Chunk failed at level:4, tier_type:0
>>> FAILED CONTIG:contig-dpp-500-500
>>>
>>> So the error seems to be pointing at something happening when wrapping
>>> up the ESTs.
>>>
>>> Seth Munholland, B.Sc.
>>> Department of Biological Sciences
>>> Rm. 304 Biology Building
>>> University of Windsor
>>> 401 Sunset Ave. N9B 3P4
>>> T: (519) 253-3000 Ext: 4755
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>
>>>
>>>
>>
>
>
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