[ensembl-dev] mysqlimport stuck on human variation

[Liu, Mingyi]

Hi,

For Ensembl83 in house installation, I downloaded all mysql files and ran the import commands. It always gets stuck on this step:

mysqlimport -P xxxx -L -h xxxx -u root -pxxxx homo_sapiens_variation_83_38 allele.txt

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.

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”.

Thanks,

Mingyi
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