[maker-devel] Failed while polishing ESTs

[Seth Munholland]

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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