Entering edit mode
11.0 years ago
2011101101
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110
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 ?
verify that you can actually open that file that is mentioned there, this pretty much sounds like a path/permission error
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
either way you should show the entire command line as you invoke it not just some small subset that you think matters.
ok . the entire command line is
RepeatMasker -nolow -no_is -norna -noint -engine wublast xaa.fa
what happens if you type:
I still think that your program just can't write to the directory in question to build the index
``Now,there is the two options of RepeatMasker
Can you tell me are the two options(
-nolow -noint
)in conflict ?