RepeatMasker bases masked is too slow

Question

[543541656]

hello,why my marked repeat is very slow after the following command

RepeatMasker -pa 4 -species rice -dir ./ ../ragtag/ragtag_output/ragtag.scaffolds.fasta.original

and my result is like this ,is there any wrong with my parameter?my library is Dfam 3.3

  Title    : Dfam
  Version  : 3.3
  Date     : 2020-11-09
  Families : 273,693



==================================================
file name: ragtag.scaffolds.fasta.original
sequences:           386
total length:  378976604 bp  (378955104 bp excl N/X-runs)
GC level:         43.58 %
bases masked:   10548985 bp ( 2.78 %)
==================================================
               number of      length   percentage
               elements*    occupied  of sequence
--------------------------------------------------
Retroelements            0            0 bp    0.00 %
   SINEs:                0            0 bp    0.00 %
   Penelope              0            0 bp    0.00 %
   LINEs:                0            0 bp    0.00 %
    CRE/SLACS            0            0 bp    0.00 %
     L2/CR1/Rex          0            0 bp    0.00 %
     R1/LOA/Jockey       0            0 bp    0.00 %
     R2/R4/NeSL          0            0 bp    0.00 %
     RTE/Bov-B           0            0 bp    0.00 %
     L1/CIN4             0            0 bp    0.00 %
   LTR elements:         0            0 bp    0.00 %
     BEL/Pao             0            0 bp    0.00 %
     Ty1/Copia           0            0 bp    0.00 %
     Gypsy/DIRS1         0            0 bp    0.00 %
       Retroviral        0            0 bp    0.00 %

DNA transposons          0            0 bp    0.00 %
   hobo-Activator        0            0 bp    0.00 %
   Tc1-IS630-Pogo        0            0 bp    0.00 %
   En-Spm                0            0 bp    0.00 %
   MuDR-IS905            0            0 bp    0.00 %
   PiggyBac              0            0 bp    0.00 %
   Tourist/Harbinger     0            0 bp    0.00 %
   Other (Mirage,        0            0 bp    0.00 %
    P-element, Transib)

Rolling-circles          0            0 bp    0.00 %

Unclassified:            3          183 bp    0.00 %

Total interspersed repeats:         183 bp    0.00 %


Small RNA:               0            0 bp    0.00 %

Satellites:              0            0 bp    0.00 %
Simple repeats:     165142      9077662 bp    2.40 %
Low complexity:      27495      1471140 bp    0.39 %
==================================================

* most repeats fragmented by insertions or deletions
  have been counted as one element


The query species was assumed to be rice          
RepeatMasker version 4.1.1 , default mode

run with rmblastn version 2.10.0+

[lieven.sterck]

do you have the rice repeat DB installed? if not it will indeed only look for the simple & low complexity repeats.

and yes, RepeatMasker is notoriously slow ... one way to speed it up is to run each scaffold/Contig seperately, that way you can 'parallelise' it a bit.