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

[Scott Geib]

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/scaffold1_datastore/B8/E3/scaffold00001//theVoid.scaffold00001/UniRef90_UPI000194D3FC.for.1588546-1589203.9.fasta
-t
/data0/opt/GenePrediction/maker/bdor/makercustom/scaffold1.maker.output/scaffold1_datastore/B8/E3/scaffold00001//theVoid.scaffold00001/scaffold00001.1588546-1589203.9.fasta
-Q protein -T dna -m protein2genome --softmasktarget  --percent 20
--showcigar  >
/data0/opt/GenePrediction/maker/bdor/makercustom/scaffold1.maker.output/scaffold1_datastore/B8/E3/scaffold00001//theVoid.scaffold00001/scaffold00001.1588546-1589203.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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