<div dir="ltr">Hello,<div><br></div><div><span style="font-size:12.8px">One possible reason is the the temporary filesystem which MySQL uses is not large enough</span><span style="font-size:12.8px"> </span><span style="font-size:12.8px">to contain the temporary files. This is set with </span><span style="font-size:12.8px">the tmpdir= parameter in the my.cnf MySQL configuration file on your MySQL server. If your tmpdir is set to /tmp and you're on a system which reveals via df that /tmp is a small tmpfs type affair it may well be worth changing it.</span></div><div><span style="font-size:12.8px"><br></span></div><div><span style="font-size:12.8px">You may also try setting the </span><span style="font-size:12.8px">myisam_sort_buffer_size and myisam_max_sort_file_size parameters to higher values before starting the import.</span></div><div><span style="font-size:12.8px"><br></span></div><div><span style="font-size:12.8px">Regards</span></div><div><span style="font-size:12.8px"><br></span></div><div><span style="font-size:12.8px">Will McLaren</span></div><div>Ensembl Variation</div></div><div class="gmail_extra"><br><div class="gmail_quote">On 15 January 2016 at 21:03, Liu, Mingyi <span dir="ltr"><<a href="mailto:Mingyi.Liu@bms.com" target="_blank">Mingyi.Liu@bms.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">Hi,<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">For Ensembl83 in house installation, I downloaded all mysql files and ran the import commands. It always gets stuck on this step:<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">mysqlimport -P xxxx -L -h xxxx -u root -pxxxx homo_sapiens_variation_83_38 allele.txt<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">I noticed that the speed of import was initially fairly fast but slows to a crawl as the import continues for many hours - typically 3 days stuck on this import
would still only import 30 GB of the 50GB of data and it just goes slower and slower and may never finish. I redid the step completely a couple times and the same issue. I then modified the homo_sapiens_variation_83_38.sql to get rid of all the 4 indices on
the allele table and still the same thing.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">Anyone else seeing this? Our mysql is “mysql Ver 14.12 Distrib 5.0.45, for redhat-linux-gnu (x86_64) using readline 5.0”.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">Thanks,<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">Mingyi<u></u><u></u></span></p>
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