Falty refseq table download for hg19

[biom...@yahoo.de]

Hello,

In order to spare server-traffic for your mysql-server I've been mirroring the most heavily used database-tables

for usage on a local mysql-server as described on your website:

sudo rsync -v -r rsync://hgdownload.cse.ucsc.edu/mysql/hg19/refGene* /var/lib/mysql/hg19/

This worked fine so far, however the current version of the hg19 refGene table seems to be buggy.

When accessed locally it causes the MySQL Server to hang forever. I checked the table using

"check table refGene;"

which gives me

| hg19.refGene | check | warning  | 1 client is using or hasn't closed the table properly |
| hg19.refGene | check | Error    | File './hg19/refGene.frm' not found (Errcode: 13)     |
| hg19.refGene | check | status   | Table is already up to date                                         |

Since /var/lib/mysql/hg19/refGene.frm is present and not empty I assume there is a problem with the original file on the download server.

The error does not occur accessing your public mysql-server, so you might just have to make a fresh copy of the three refGene table files to the download location (hgdownload.cse.ucsc.edu/mysql/hg19/).

Could you check that?

Thanks a lot for help again :-)

Mark

[Pauline Fujita]

Hello Mark,

We think we might have corrected the issue. If you are still having
trouble with this please contact the mailing list again at
gen...@soe.ucsc.edu.

Best regards,

Pauline Fujita
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu

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[biom...@yahoo.de]

Hello,

I've come across an error mirroring the refseq-tables from your public mysql-server.

I had reported the very same error earlier (see below) and you corrected it successfully in the meantime.

Now it is occuring again.

I assume there is some problem with the way the tables are updated.

It's a bit strange that the error is in the same file of the same table as previously.

Thanks and best wishes,

Arno

----- Weitergeleitete Message -----
Von: "biom...@yahoo.de" <biom...@yahoo.de>
An: "gen...@soe.ucsc.edu" <gen...@soe.ucsc.edu>
Gesendet: 17:05 Donnerstag, 4.April 2013
Betreff: Falty refseq table download for hg19

[Pauline Fujita]

Hello Arno,

Thank you for reporting this problem. We think we have fixed the
issue. Please contact the mailing list again at gen...@soe.ucsc.edu if
the problem persists.

Best regards,

Pauline Fujita
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu

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[biom...@yahoo.de]

Hello,

I have again come across the problem with a faulty mysql refGene table for hg19 from the download server.

I have reported the very same error twice before and it got fixed both times (see below).

Since keeps re-appearing I suspect that there is an error in some script that generates the table or copies it to the download server.

Thanks a lot for the invaluable services you provide to the whole community!

Greetings,

Arno

>Arno
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[Steve Heitner]

Hello, Arno.

Thank you for informing us again of this problem.  We have hopefully fixed it for good this time, but please do let us know if you encounter the problem again.

Please contact us again at gen...@soe.ucsc.edu if you have any further questions.  Questions sent to that address will be archived in a publicly-accessible forum for the benefit of other users.  If your question contains sensitive data, you may send it instead to genom...@soe.ucsc.edu.

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Steve Heitner
UCSC Genome Bioinformatics Group

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