Question: A Question About Repeatmasker'S Parameters
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gravatar for 2011101101
7.7 years ago by
2011101101100
2011101101100 wrote:

The nature article Draft genome of the wheat A-genome progenitor Triticum urartu use the RepeatMasker to analysis repetitive elements .when I use the RepeatMasker's parameters as the article ,there is an error. The parameters used in RepeatMasker were as follows:

-nolow -no_is -norna -noint -engine wublast

The error in below

 analyzing file xaa.fa
CrossmatchSearchEngine::parseOutput: Unable to open results file: 
/export/soft/miRDeep_star/build_bwt_idx_v2/genome_test/RM_25295.WedApr32253392013/xaa.fa_batch-1.cat : 没有那个文件或目录 at /usr/local/RepeatMasker/CrossmatchSearchEngine.pm line 529.WARNING: Retrying batch ( 1 ) [ 2,, 61194]...

when I used -nolow -noint alone ,there is no error .I think the two parameters in conflict as the RepeatMasker manual . If it's true ,the nature article has a wrong description .Is it possible ?

repeatmasker • 2.7k views
ADD COMMENTlink modified 6.6 years ago by Biostar ♦♦ 20 • written 7.7 years ago by 2011101101100

verify that you can actually open that file that is mentioned there, this pretty much sounds like a path/permission error

ADD REPLYlink written 7.7 years ago by Istvan Albert ♦♦ 85k

There is no such file like xaa.fa_batch-1.cat.Anyone can try it,if I'm wrong ,it can run ok in other compute

ADD REPLYlink written 7.7 years ago by 2011101101100

either way you should show the entire command line as you invoke it not just some small subset that you think matters.

ADD REPLYlink written 7.7 years ago by Istvan Albert ♦♦ 85k

ok . the entire command line is RepeatMasker -nolow -no_is -norna -noint -engine wublast xaa.fa

ADD REPLYlink modified 7.7 years ago • written 7.7 years ago by 2011101101100

what happens if you type:

touch /export/soft/miRDeep_star/build_bwt_idx_v2/genome_test/RM_25295.WedApr32253392013/xaa.fa_batch-1.cat

I still think that your program just can't write to the directory in question to build the index

ADD REPLYlink written 7.7 years ago by Istvan Albert ♦♦ 85k

``Now,there is the two options of RepeatMasker

-nolow /-low
    Does not mask low_complexity DNA or simple repeats

-noint /-int
    Only masks low complex/simple repeats (no interspersed repeats)

Can you tell me are the two options(-nolow -noint )in conflict ?

ADD REPLYlink modified 7.7 years ago • written 7.7 years ago by 2011101101100
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