[maker-devel] can't call method strand on an undefined value ERROR: Failed while flattening protein clusters

[Carson Holt]

Use this command to check out the latest unreleased test version, and lt me
know if you still get the error.

Command -->  svn co svn://malachite.genetics.utah.edu/maker/trunk maker

User: yandell_guest
Password: y at ndell_Gu3st

Thanks,
Carson





From:  Scott Geib <smg283 at gmail.com>
Date:  Tuesday, 22 May, 2012 2:42 AM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] can't call method strand on an undefined value
ERROR: Failed while flattening protein clusters

Hi, 
Using maker 2.24, I am getting the following error (see below) in
protein2genome widget.  I also get the same error with est2genome.  This
happens with my own data (testing on a single scaffold), but not with the
test data supplied with maker (dpp files in data folder).
Scott


Widget::exonerate::protein2genome:
/data0/opt/AlignmentSoftware/exonerate/exonerate-2.2.0-x86_64/bin/exonerate
-q 
/data0/opt/GenePrediction/maker/bdor/makercustom/scaffold1.maker.output/scaf
fold1_datastore/B8/E3/scaffold00001//theVoid.scaffold00001/UniRef90_UPI00019
4D3FC.for.1588546-1589203.9.fasta -t
/data0/opt/GenePrediction/maker/bdor/makercustom/scaffold1.maker.output/scaf
fold1_datastore/B8/E3/scaffold00001//theVoid.scaffold00001/scaffold00001.158
8546-1589203.9.fasta -Q protein -T dna -m protein2genome --softmasktarget
--percent 20 --showcigar  >
/data0/opt/GenePrediction/maker/bdor/makercustom/scaffold1.maker.output/scaf
fold1_datastore/B8/E3/scaffold00001//theVoid.scaffold00001/scaffold00001.158
8546-1589203.UniRef90_UPI000194D3FC.p_exonerate.9
#-------------------------------#
cleaning blastx...
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
 ...processing 0 of 23
 ...processing 1 of 23
 ...processing 2 of 23
 ...processing 3 of 23
 ...processing 4 of 23
 ...processing 5 of 23
 ...processing 6 of 23
 ...processing 7 of 23
 ...processing 8 of 23
 ...processing 9 of 23
 ...processing 10 of 23
 ...processing 11 of 23
 ...processing 12 of 23
 ...processing 13 of 23
 ...processing 14 of 23
 ...processing 15 of 23
 ...processing 16 of 23
 ...processing 17 of 23
 ...processing 18 of 23
 ...processing 19 of 23
 ...processing 20 of 23
 ...processing 21 of 23
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
 ...processing 0 of 20
 ...processing 1 of 20
 ...processing 2 of 20
 ...processing 3 of 20
 ...processing 4 of 20
 ...processing 5 of 20
 ...processing 6 of 20
 ...processing 7 of 20
 ...processing 8 of 20
 ...processing 9 of 20
 ...processing 10 of 20
 ...processing 11 of 20
 ...processing 12 of 20
 ...processing 13 of 20
 ...processing 14 of 20
 ...processing 15 of 20
 ...processing 16 of 20
 ...processing 17 of 20
 ...processing 18 of 20
total clusters:2 now processing 0
Can't call method "strand" on an undefined valueERROR: Failed while
flattening protein clusters
ERROR: Chunk failed at level:11, tier_type:2
FAILED CONTIG:scaffold00001

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