<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif;"><div>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).</div><div><br></div><div>Then count the number of FINISHED entries in the log.</div><div><br></div><div>Thanks,</div><div>Carson</div><div><br></div><div><br></div><div><br></div><span id="OLK_SRC_BODY_SECTION"><div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt"><span style="font-weight:bold">From: </span> Rebecca Harris <<a href="mailto:rebzi87@gmail.com">rebzi87@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Tuesday, February 4, 2014 at 3:29 PM<br><span style="font-weight:bold">To: </span> <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> [maker-devel] maker output<br></div><div><br></div><div dir="ltr">Hi,<div><br></div><div>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. </div><div><br></div><div>Thanks!</div><div><br></div><div>Cheers,</div><div>Rebecca</div></div>
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