[maker-devel] Avoiding re-indexing the same file

[Carson Holt]

MAKER only indexes the input files during the first run. It will reuse the indexes after that. The indexes are in the *.maker.output.mpi_blastdb directory. If this is a repeatmasker issue, it keeps it’s indexes under the …/RepeatMasker/Libraries/ directory and reuses them after indexing the first time.

—Carson



> On Jan 29, 2020, at 7:42 AM, H.DENISE <had38 at cam.ac.uk> wrote:
> 
> Hi,
> I’m new to Maker and need to compare the annotations with different features (+/- RepeatMasker, using different protein files etc …). However the first step seems to be the indexing of my files and the RNASeq file I’m using is large, therefore Maker seems to take ages at this step,. As it is a constant file for my applications, is there a way to provide the indexing file in order to avoid repeating this step?
> Thanks in advance, Hubert
> 
> 
> 
> Hubert DENISE, PhD
> 
> Genome Data Analyst
> R.Durbin's group
> Department of Genetics
> University of Cambridge
> 
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