MAKER v3 ERROR: Failed while processing all repeats

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MAKER v3 ERROR: Failed while processing all repeats


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 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/ line 188.

--> rank=1,

ERROR: Failed while processing all repeats

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



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




Kapeel Chougule
Computational Scientist Developer II
One Bungtown Road Cold Spring Harbor, NY 11724

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