[Gmod-help] Problem with mysql: ERROR 29 (HY000) at line 1: File '/tmp/fdata.9150' not found (Errcode: 13)

[Scott Cain]

Hi Philipp,

Did you grant file permissions to your mysql user?  Just "GRANT ALL"
is not sufficient; in mysql, file permissions are separate and have to
be granted explicitly.

Scott


On Wed, Jun 15, 2011 at 4:24 PM, Philipp Schiffer
<p.schiffer at uni-koeln.de> wrote:
> Hi!
>
> While GBrose2 is running smoothly on my Ubuntu 11.04 machine using the
> berkeley db I am having troubles setting it up with mysql (basically the
> same happened under Ubuntu 10.10 before I switched to berkeley, however now
> I have more data). When I do the
> bp_bulk_load_gff.pl -d m_FREEZE_1_sub -u xyz -p "xyz"
> predictionsubset_gff/maker_FREEZE_rom1.predictionsubset.gff
> I end up with this error:
> ERROR 29 (HY000) at line 1: File '/tmp/fdata.9150' not found (Errcode: 13)
>
> That file however exists transiently in /tmp along with all the scaffolds
> taken from my gff: ls -l /tmp
> -rw-r--r-- 1 philipp philipp 2709484 Jun 15 22:18 fdata.9239
> -rw-r--r-- 1 philipp philipp       0 Jun 15 22:18 fdna.9239
>
> The files disappears along with the scaffolds, but I couldn't make out the
> exact moment yet. Is the bulk script somehow shooting itself?
>
> Regards,
>
> Philipp
> --
> Philipp Schiffer
>
> Email: p.schiffer at uni-koeln.de
> http://www.mathnat.uni-koeln.de/10803.html
>
> Universität zu Köln
>
> Zoologisches Institut
> AG Experimentelle Morphologie
> Prof. Dr. Schierenberg
> Biozentrum Köln
> Zülpicher Straße 47b
> 50674 Köln, Germany
> Tel.: +49 (0)221 4704326
> Fax: +49 (0)221 4704987
>
> und ehemals
>
> Institut für Geologie und Mineralogie
> AG Paläontologe und Historische Geologie
> Prof. Dr. Herbig
> Zülpicher Straße 49a
> D-50674 Köln, Germany
> Tel.: +49 (0)221 4701640
> Fax: +49 (0)221 4705080
>
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research