error with Snap

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error with Snap

Matthew Conte
Hello,

I'm running Maker with trained Snap.  For the most part it seems to work, but a few scaffolds (~0.1%) are giving me an error with Snap.  For example:

#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /raid/maker_runs/scaffolds_v1/gff/all_scaffolds.hmm -xdef /raid/maker_runs/scaffolds_v1/assembly.maker.output/assembly_datastore/17/54/scaffold_7//theVoid.scaffold_7/607_0.7625970-7628711.all_scaffolds.hmm.auto_annotator.xdef.snap  /raid/maker_runs/scaffolds_v1/assembly.maker.output/assembly_datastore/17/54/scaffold_7//theVoid.scaffold_7/607_0.7625970-7628711.all_scaffolds.hmm.auto_annotator.snap.fasta > /raid/maker_runs/scaffolds_v1/assembly.maker.output/assembly_datastore/17/54/scaffold_7//theVoid.scaffold_7/607_0.7625970-7628711.all_scaffolds.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /usr/local/bin/snap): zoeVerifyFeature: start > end
Coding  2541    2540    -       0.200   .       .       .       ADJ
ZOE ERROR (from /usr/local/bin/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed

FATAL ERROR
ERROR: Failed while annotating transcripts!!

ERROR: Chunk failed at level 19
!!
FAILED CONTIG:scaffold_7


It seems obvious from the error and the 607_0.7625970-7628711.all_scaffolds.hmm.auto_annotator.xdef.snap file that an illegal feature is predicted by Snap.  I'm unsure why this is the case and/or how to fix this.  Has anyone seen this error before or have any suggestions?

Thanks,
Matt

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Re: error with Snap

Carson Hinton Holt
Re: [maker-devel] error with Snap Never seen it. Could you send me the dataset you used to generate the error?

Thanks,
Carson


On 3/11/11 9:06 AM, "Matthew Conte" <mconte@...> wrote:

Hello,

I'm running Maker with trained Snap.  For the most part it seems to work, but a few scaffolds (~0.1%) are giving me an error with Snap.  For example:

#--------- command -------------#
Widget::snap:
/usr/local/bin/snap -minus /raid/maker_runs/scaffolds_v1/gff/all_scaffolds.hmm -xdef /raid/maker_runs/scaffolds_v1/assembly.maker.output/assembly_datastore/17/54/scaffold_7//theVoid.scaffold_7/607_0.7625970-7628711.all_scaffolds.hmm.auto_annotator.xdef.snap  /raid/maker_runs/scaffolds_v1/assembly.maker.output/assembly_datastore/17/54/scaffold_7//theVoid.scaffold_7/607_0.7625970-7628711.all_scaffolds.hmm.auto_annotator.snap.fasta > /raid/maker_runs/scaffolds_v1/assembly.maker.output/assembly_datastore/17/54/scaffold_7//theVoid.scaffold_7/607_0.7625970-7628711.all_scaffolds.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /usr/local/bin/snap): zoeVerifyFeature: start > end
Coding  2541    2540    -       0.200   .       .       .       ADJ
ZOE ERROR (from /usr/local/bin/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed

FATAL ERROR
ERROR: Failed while annotating transcripts!!

ERROR: Chunk failed at level 19
!!
FAILED CONTIG:scaffold_7


It seems obvious from the error and the 607_0.7625970-7628711.all_scaffolds.hmm.auto_annotator.xdef.snap file that an illegal feature is predicted by Snap.  I'm unsure why this is the case and/or how to fix this.  Has anyone seen this error before or have any suggestions?

Thanks,
Matt


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