[BioSQL-l] Problems with installation Biosql

[Peter]

Hi,

Don't forget to CC the mailing list on replies ;)

On Tue, Jan 19, 2010 at 9:42 AM, Piotr Borowiec <piotrborowiec at g.pl> wrote:
>
> Thanks for advice. I gave the script all parameters and next there was
> a message:
>
> Loading NCBI taxon database in taxdata:
>        ... retrieving all taxon nodes in the database
>        ... reading in taxon nodes from nodes.dmp
> Couldn't open data file taxdata/nodes.dmp: No such file or directory
> rollback ineffective with AutoCommit enabled at load_ncbi_taxonomy.pl line 841.
> Use of uninitialized value in concatenation (.) or string at
> load_ncbi_taxonomy.pl line 843.

The script has an option to download the taxonomy file from
the NCBI (--download true), or to use an existing copy (e.g.
from a previous run). I suspect that you have a partial copy
from an aborted run which is confusing the script. I would try
again explicitly asking for a fresh download. I would also try
removing the taxdata directory (if present) and any (partial)
taxdata archive file - then try again.

Peter