[maker-devel] maker output

[Carson Holt]

Clusters are notoriously flakey, so maker is restartable (hence the need for
the log file).  Also since multiple nodes may write simultaneously to the
log, they can munge it’s contents.   You can rerun maker with the -dsindex
flag to regenerate the master_datastore_index.log as well without processing
anything else. You can even delete it before rebuilding it if you want to
ensure all entries are uniq (run on a single cpus when you do this).

Then count the number of FINISHED entries in the log.

Thanks,
Carson



From:  Rebecca Harris <rebzi87 at gmail.com>
Date:  Tuesday, February 4, 2014 at 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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