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.