Question about maker. Maker2 failed

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Question about maker. Maker2 failed

祖尧刘

Hi maker developers


I'm using maker 2 to annotate a fish genome.

When I try to provide rm_gff file, it always fails.

Here is log:



collecting blastx repeatmasking
doing repeat masking
processing all repeats
deleted:0 hits
in cluster::shadow_cluster...
Died at /gpfs/homefs/iee/zl19g775/miniconda3/envs/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 188.
--> rank=23, hostname=hnode48
ERROR: Failed while processing all repeats
ERROR: Chunk failed at level:3, tier_type:1
FAILED CONTIG:chr_XXIII

ERROR: Chunk failed at level:2, tier_type:0
FAILED CONTIG:chr_XXIII

I use maker 2.3.10 with repeatmasker 4.0.9.
I saw someone got this error as well and I followed the solutions.
I  tried update to blast 2.9.0, rmblast 2.9.0,bioperl1.7.7 and also checked rm gff file with gff3 validator. But the error still existed.

Do you have any suggestions?

Thanks a lot for your help.



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