[ensembl-dev] problem installing ensembl_compara_61

[Hardip Patel]

Hi All

I am also getting the same issue with mouse core data v61.

however, in my case, it stops at the first file.

After reading about it on the web, it seems like older versions of mysql had some issues with mysqlimport.

see details that are related to the bug at http://bugs.mysql.com/bug.php?id=5829

I am not sure if it is the case at all or not.

Any help is greatly appreciated.

Thanking you.

Kind regards

Hardip


On 13/04/11 3:43 PM, "Jeff Hussmann" <jeff.hussmann at gmail.com> wrote:

Hello all -

I am trying to install a local mysql copy of ensembl_compara_61. Everything goes fine until my script attempts to import the file peptide_align_feature_mus_musculus_57.txt into mysql (as part of executing the command "mysqlimport -u root --password=$password --fields_escaped_by=\\ $database -L $base_directory/$database/*.txt #>> $log_file_name") at which point I get the error message

"mysqlimport: Error: 1016, Can't open file: './ensembl_compara_61/peptide_align_feature_mus_musculus_57.frm' (errno: 24), when using table: peptide_align_feature_mus_musculus_57".

Every peptide_align_feature_*.txt alphabetically before mus_musculus imports without complaint (and installation of ensembl_compara_60 several months ago on a different machine went smoothly).

Any idea what is going wrong?

 - Jeff

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--
Hardip R. Patel, PhD
Bioinformatician, Molecular Genetics Division,
Victor Chang Cardiac Research Institute,
Darlinghurst, NSW - 2010, Australia
(W): +61 - 2 - 9295 8611
(M): 0449 180 715

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