repeatmodeler

项目地址 https://github.com/Dfam-consortium/RepeatModeler

基本使用¶

$ module load arm/repeatmodeler/2.0.6 

# Create a Database for RepeatModeler
$ BuildDatabase -name elephant elephant.fa

# Run RepeatModeler
$ RepeatModeler -database elephant   -threads 20 -LTRStruct

运行报错¶

build_lmer_table 运行出错，这是 RepeatScout 中的工具，需要修改 2 行代码，然后重新编译，具体见 Commit c5193bb

RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 2674090 bp ( 2673946 non ambiguous )
   - Num Contigs Represented = 188
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 12 )..
build_lmer_table failed. Exit code 256

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