No results of RepeatProteinMasker

Question

[yangyongzhi2008]

Hello everyone,

I was trying to run the RepeatProteinMasker with the newest Libraries (repeatmaskerlibraries-20150807.tar.gz). But I got no result of this software. The command line is below:

/home/share/tools/genome_annotation/RepeatMasker/RepeatMasker/RepeatProteinMask -engine ncbi -noLowSimple -pvalue 1e-04 Final.assembly.fa

Identifying Simple and Low Complexity Repeats...(masking turned off)
   - Tandem Repeats: 341894
Masking Repeat Proteins...
   - Protein Hits = 0
Done!

I doubt that there is a special library of RepeatProteinMasker, but I am not sure. So, anyone could help me?

Answer 1

[yangyongzhi2008]

Change the RMblast with the ABblast, everything has been resolved.

Answer 2

[wn1364]

hi,i want to know how large about your genome? and how long did u run? i anotate a genome about ~2G,and i have been running for 8 days..it still not unfinish...

[Bart Ulaszewski]

In general it depends on the number of cores used for an analysis. In my case when I've used 3 CPU's it took 7 day to mask a 450 Mbp genome, on the other hand with 40 CPU's 850Mbp genome was masked within 12 hrs.