Inconsistent RepeatMasker error on draft assembly

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Inconsistent RepeatMasker error on draft assembly

Zach Cohen
Hello All,
I'm receiving a RepeatMasker on some (not all) of my scaffolds. 

Widget::RepeatMasker:

cd /tmp/maker_7hGhhm; /scratch/exe/RepeatMasker/RepeatMasker /scratch/bin/or_test3.maker.output/or_test3_datastore/E3/2F/scaffold2852_size18614//theVoid.scaffold2852_size18614/0/scaffold2852_size18614.0.all.rb -species all -dir /scratch/bin/or_test3.maker.output/or_test3_datastore/E3/2F/scaffold2852_size18614//theVoid.scaffold2852_size18614/0 -pa 2

#-------------------------------#

ERROR: RepeatMasker failed

--> rank=NA, hostname=82853d8df2a5

ERROR: Failed while doing repeat masking

ERROR: Chunk failed at level:0, tier_type:1

FAILED CONTIG:scaffold2852_size18614

ERROR: Chunk failed at level:2, tier_type:0

FAILED CONTIG:scaffold2852_size18614

examining contents of the fasta file and run log


I'm not sure if there is an issue with the widget itself, as this doesn't come up for all the scaffolds and the example data seemed to run fine, or a problem with these particular scaffolds. Thanks for any assistance you can provide!

Best,

Z


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Re: Inconsistent RepeatMasker error on draft assembly

Carson Holt-2
If running under MPI, you can get messages from multiple processes (slightly out of order), in which case the more descript cause of the error may be further upstream in the STDERR log. If running without MPI, and the error you see is matched with the Widget::RepeatMasker command used, then you can simply copy it and run it outside of MAKER. If there are installation issues with your RepeatMasker copy then the cause will become more apparent.

i.e. Run the command by itself —> /scratch/exe/RepeatMasker/RepeatMasker /scratch/bin/or_test3.maker.output/or_test3_datastore/E3/2F/scaffold2852_size18614//theVoid.scaffold2852_size18614/0/scaffold2852_size18614.0.all.rb -species all -dir /scratch/bin/or_test3.maker.output/or_test3_datastore/E3/2F/scaffold2852_size18614//theVoid.scaffold2852_size18614/0 -pa 2

—Carson


On Aug 11, 2017, at 12:43 PM, Zach Cohen <[hidden email]> wrote:

Hello All,
I'm receiving a RepeatMasker on some (not all) of my scaffolds. 

Widget::RepeatMasker:

cd /tmp/maker_7hGhhm; /scratch/exe/RepeatMasker/RepeatMasker /scratch/bin/or_test3.maker.output/or_test3_datastore/E3/2F/scaffold2852_size18614//theVoid.scaffold2852_size18614/0/scaffold2852_size18614.0.all.rb -species all -dir /scratch/bin/or_test3.maker.output/or_test3_datastore/E3/2F/scaffold2852_size18614//theVoid.scaffold2852_size18614/0 -pa 2

#-------------------------------#

ERROR: RepeatMasker failed

--> rank=NA, hostname=82853d8df2a5

ERROR: Failed while doing repeat masking

ERROR: Chunk failed at level:0, tier_type:1

FAILED CONTIG:scaffold2852_size18614

ERROR: Chunk failed at level:2, tier_type:0

FAILED CONTIG:scaffold2852_size18614

examining contents of the fasta file and run log


I'm not sure if there is an issue with the widget itself, as this doesn't come up for all the scaffolds and the example data seemed to run fine, or a problem with these particular scaffolds. Thanks for any assistance you can provide!

Best,

Z

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maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


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[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org