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

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

Debug export is still going... 2.5GB of log files so far with progress at
65%...

I posted the link of the WARN log on the plasmodium page here:
https://www.cs.lmu.edu/biodb/fall2010/index.php/Plasmodium_falciparum.
Richard
On Fri, Mar 11, 2011 at 1:06 PM, Richard Brous <rbr...@gm...> wrote:

> 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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>