[maker-devel] maker output

[Daniel Ence]

Hi Rebecca, If you're looking at the master_datastore_index.log, then you're looking for lines with the "FINISHED" status. If you do a count on those (with "grep -c" for example), that will tell you how many contigs have finished.

If you have 200,000,000 contigs that you're trying to annotate, you might also consider settinng the "min_contig" parameter in the maker_opts.ctl file. This parameter sets a minimum length for a contig before MAKER tries to annotate it. Usually 5000 bp or larger is what you want. That will save you some time in the long run.

Thanks,
Daniel

Daniel Ence
Graduate Student
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330
________________________________
From: maker-devel [maker-devel-bounces at yandell-lab.org] on behalf of Rebecca Harris [rebzi87 at gmail.com]
Sent: Tuesday, February 04, 2014 3:29 PM
To: maker-devel at yandell-lab.org
Subject: [maker-devel] maker output

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. 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.

Thanks!

Cheers,
Rebecca
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