Re: [XMLPipeDB-developer] Plasmodium bug/task list

[Richard B. <rbr...@gm...>]

Hi all,

Have been working through several Plasmodium gdb exports in an attempt to
source why only one gene id makes it into the Ordered Locus table.

I have reviewed the logger file while set to "WARN" and wasn't able to
determine anything which would suggest an error. I will post this log file
to the wiki later today when I get home.

I then upped the logger verbosity to "DEBUG" and file size to 100MB with
hopes that more detail will surface the issue, but my export is on hour 20
and still going (although its nearly complete). What I didn't expect was the
size of the log files and that it seems only the last 3 are kept with
earlier logs being overwritten =( I fear that the information I need it in
one of the earlier files which are now lost.

Unless a better suggestion is offered I'm going to rerun an export again
with 'DEBUG" verbosity and up the file sizes to near 1 GB each and hope that
3 GB total will be enough to hold the complete export log.

More info as it comes...

Richard





On Fri, Mar 4, 2011 at 3:17 PM, Kam Dahlquist <kda...@lm...> wrote:

> Hi,
>
> I've completed testing the Plasmodium gdb I exported last November and
> updated the SourceForge wiki.
>
> Plasmodium has it's own task list page, which I've updated here:
> https://sourceforge.net/apps/mediawiki/xmlpipedb/index.php?title=Plasmodium_falciparum_Task_List
>
> The testing report can be found here:
> https://sourceforge.net/apps/mediawiki/xmlpipedb/index.php?title=Gene_Database_Testing_Report_P._falciparum_20101115
>
> The source files and gdb are on a new Plasmodium falciparum page on the
> Fall 2010 BiolDB wiki:
> https://www.cs.lmu.edu/biodb/fall2010/index.php/Plasmodium_falciparum
>
> Here is the list of bugs/action items that I've listed:
>
> 1.  The OrderedLocusNames table in the gdb only has 1 ID out of 5345
> repored by the TallyEngine. This also affects all other tables related to
> OrderedLocusNames.
>
> 2.  The GeneId table in the database has 6 fewer IDs than reported by the
> TallyEngine (*Mycobacterium smegmatis* and *Mycobacterium tuberculosis*also have mysterious GeneId issues with the TallyEngine).
>
> 3.  The count for EMBL IDs in the gdb also seems low, it's lower than the
> 2009 version of the gdb. There's no way to tell at this point whether this
> is due to a change in annotation by UniProt or is a bug with GenMAPP
> Builder.
>
> Thanks,
> Kam
>
>
>
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