[maker-devel] maker output

Tue Feb 4 15:49:46 MST 2014

> 4 feb 2014 kl. 23:32 skrev "Rebecca Harris" <rebzi87 at gmail.com>:
> 
> Hi,
> 
> I'm running maker on a cluster and am having some problems with the run ending prematurely. I would like to know if there is a straightforward way to figure out whether maker has completed. I've tried: 1) counting the number of run.log files in the datastore directly, and 2) counting the instances of "FINISHED" in the master_datastore_index.log.

This is usually what I do to check if maker has finished all scaffolds. There should be one FINISHED statement for each entry in the scata file. (It might be one for every scaffold longer than the gjven minimum length. 

> These numbers are inconsistent. I have 200,000 contigs in my fasta file - do I expect 200,000 run.log files? I've had to restart maker a few times - it appears that maker is appending to the master_datastore_index.log, as I find multiple instances of the same contig being finished. 

Run maker -daindex to rebuild the file if you like. The number of FINISHED should not change though

Mikael

> 
> Thanks!
> 
> Cheers,
> Rebecca
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