[maker-devel] Failed while polishing ESTs

[Seth Munholland]

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
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