[maker-devel] MAKER v3 ERROR: Failed while processing all repeats

[Kapeel Chougule]

Hi,

I am using MAKER v3 to update community annotation with new RNA-seq
evidence data. Part of my problem is that MAKER shows below error when
repeat masking. I have attached the community annotation gff, maker log and
maker_opts.ctl for your reference.  I searched for this error  in the
maker-dev google group and found some hints
<https://groups.google.com/forum/#!topic/maker-devel/651ka80F3s4> to update
BLAST to 2.7, rmblast to 2.6 and reconfigure RepeatMasker which I did but
it still fails with the error. Any help appreciated.

deleted:0 hits

collecting blastx repeatmasking

processing all repeats

in cluster::shadow_cluster...

Died at /mnt/grid/ware/hpc/home/data/mcampbel/applications/maker/
bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 188.

--> rank=1, hostname=bnbcompute15.blacknblue.cshl.edu

ERROR: Failed while processing all repeats

ERROR: Chunk failed at level:3, tier_type:1

FAILED CONTIG:Chr06



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

FAILED CONTIG:Chr06


Genome fasta:
https://de.cyverse.org/dl/d/F612A6E2-A58E-44F0-895D-B766B41FE287/Chr06.gff
MAKER_run_log:
https://de.cyverse.org/dl/d/0B898D91-1520-4D19-9835-DC7EDD52415F/maker.run.log
Maker_opts.ctl:
https://de.cyverse.org/dl/d/15EB321B-4604-47C9-8E4F-0DC8D78517CE/maker_opts.ctl

Thanks



-- 



*Kapeel ChouguleComputational Scientist Developer II*


*One Bungtown Road Cold Spring Harbor, NY 11724http://www.warelab.org/
<http://www.warelab.org/>*
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