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3.3 years ago
543541656
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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+
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.