A Question About Repeatmasker'S Parameters

Question

[2011101101]

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 ?

[Istvan Albert]

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

[2011101101]

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

[Istvan Albert]

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

[2011101101]

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

[Istvan Albert]

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

[2011101101]

``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 ?