<div dir="ltr"><div class="gmail_extra"><div class="gmail_quote"><div>Cedar</div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div class="">> My problem is that it's been running for about a month now, using 90% of memory, and 4600% cpu. In other words, it appears to be using available resources. If I read the output (pasted below) correctly, I can expect to see 6566 partitions. After a month, it is working on partition 2178, so I'm only 1/3 of the way through.<br>
</div></blockquote><div><br></div><div>My suggestion is to run "sga preqc" on the reads to get an idea if there is anything unusual about your data set:</div><div><br></div><div><a href="https://groups.google.com/forum/#!msg/sga-users/95dTwpJCARU/oKoq54EZqKwJ">https://groups.google.com/forum/#!msg/sga-users/95dTwpJCARU/oKoq54EZqKwJ</a></div>
<div><br></div><div>Torsten</div><div><br></div><div><br></div></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div class="">> The computer I'm using has 48 cores (AMD 6176 2.3Ghz) and 256GB ram.</div></blockquote><div><br></div><div>PS. We have similar: 64 cores (AMD 6272 2.1 Ghz) and 512GB RAM :-)<br></div><div><br></div>
-- <br><div dir="ltr"><font face="tahoma, sans-serif" size="1"><i>--Dr Torsten Seemann<br>--Victorian Bioinformatics Consortium, Monash University, AUSTRALIA</i></font><div><font face="tahoma, sans-serif"><i><font size="1">--Life Sciences Computation Centre, VLSCI, Parkville, AUSTRALIA<br>
--<a href="http://www.bioinformatics.net.au/" target="_blank">http://www.bioinformatics.net.au/</a></font></i><br></font></div><div><br></div></div>
</div></div>