[maker-devel] running Maker but skipping first steps

[Carson Holt]

These are just status messages. The steps don’t actually rerun, except for the control file parsing.  That obviously has to happen every time for MAKER to know the control files are still the same between runs.

Both these messages —>
STATUS: Processing and indexing input FASTA files...
STATUS: Setting up database for any GFF3 input... 

MAKER sees that the indexes already exists, validates their integrity, and then moves on.  So there is no rerunning of steps.

—Carson




> On Nov 10, 2014, at 3:35 AM, Muriel Gros-Balthazard <muriel.grosb at gmail.com> wrote:
> 
> Hello,
> 
> I want to run Maker but I would like to skip the first steps :
> STATUS: Parsing control files...
> STATUS: Processing and indexing input FASTA files...
> STATUS: Setting up database for any GFF3 input...
> A data structure will be created for you at:
> /Data/Genomics/GeneAnnotation/Maker_pipeline/5_Run_Maker/Pdac_ref2013s.maker.output/Pdac_ref2013s_datastore
> 
> To access files for individual sequences use the datastore index:
> /Data/Genomics/GeneAnnotation/Maker_pipeline/5_Run_Maker/Pdac_ref2013s.maker.output/Pdac_ref2013s_master_datastore_index.log
> 
> Indeed, there was an error in RepeatMasking (and I reinstalled RepeatMasker) but I believe that the previous steps are always the same.
> Is there a way to run Maker so that it doesn't run this first steps again given that the control files didn't change, the fasta files are already indexed and the database of gff3 is set up ?
> 
> Thank you !
> 
> Muriel
> 
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