[ensembl-dev] mysqlimport error

Andy Yates ayates at ebi.ac.uk
Thu Jul 31 09:06:31 BST 2014

Hi David,

Sorry to hear you're having trouble with this. Whilst I've not seen this problem before myself I believe it is caused by a corrupt MyISAM table. This can happen due to a system or mysqld crash. I'm sure the files are not corrupt as we have loaded them into our own MySQL instance here at the EBI (though you may want to check checksums to make sure your transfer was good). Also your command looks fine to me.

Have you dropping the compressed_genotype_region, recreating it and then attempting a re-load?



Andrew Yates - Ensembl Support Coordinator
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Cambridge CB10 1SD
Tel: +44-(0)1223-492538
Fax: +44-(0)1223-494468

On 30 Jul 2014, at 20:26, David Rhee <david.rhee at einstein.yu.edu> wrote:

> Hi all,
> I'm getting the following error when I try to load compressed_genotype_region table on homo_sapiens_variation_75_37 database.
> > mysqlimport -u username -p --fields_escaped_by=\\ homo_sapiens_variation_75_37 -v -d -L compressed_genotype_region.txt
> > Enter password: 
> > Connecting to localhost
> > Selecting database homo_sapiens_variation_75_37
> > Deleting the old data from table compressed_genotype_region
> > Loading data from LOCAL file: /data/compressed_genotype_region.txt into compressed_genotype_region
> > mysqlimport: Error: 1034, Wrong bytesec:   0-  0-  0 at 163760275876; Skipped, when using table: compressed_genotype_region
> System : Ubuntu 14.04
> MySQL : 5.5.38-0ubuntu0.14.04.1
> Ensembl : release 75
> Is this due to corruption on file itself or some sort of encoding issue? I was able to successfully load homo_sapiens_core_75_37 and homo_sapiens_funcgen_75_37 databases using the generic command "mysqlimport -u username -p --fields_escaped_by=\\ Database Name -L *.txt". 
> For homo_sapiens_variation_75_37, I was able to successfully load all tables except  compressed_genotype_var table which I'm also getting a similar Wrong bytesec error.
> Thanks in advance!
> David
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