[ensembl-dev] mysqlimport error

David Rhee david.rhee at einstein.yu.edu
Wed Jul 30 20:26:17 BST 2014

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!

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