[Go] go db issues

[Chris Mungall]

On Apr 13, 2009, at 9:15 AM, Benjamin Hitz wrote:

>
>
> Update:  This failed again this morning.  As near as I can tell, the  
> part of the sequence loading that uses esearch/efetch @ NCBI is not  
> working.  My guess (from some handrolled tests) is that esearch is  
> failing, but returing a valide WebEnv key.  That key when used with  
> efetch returns enough of genbank so as to break everything.

Perhaps send the URL & others can try. Perhaps SGD has been blocked...?

>
> I suppose I could just comment out the NCBI sequence loading...  
> that's going to lose quite a bit though.

Mostly just the rodents that lose out:
http://wiki.geneontology.org/index.php/Gp2protein#Report.2C_Mar_31.2C_2009

>  I will run a test on the dev database and give a report.
>
> Ben
>
> On Apr 10, 2009, at 3:17 PM, Benjamin Hitz wrote:
>
>> Just FYI, I am currently debugging an issue with the GOLITE  
>> sequence loading (golite load failed early this morning, this is  
>> the load that amigo uses)
>>
>> Apparently, NCBI has somehow altered their output content or format  
>> such that it runs the loader completely out of RAM - even when  
>> requesting 73 or so proteins.
>>
>> The command in question is:
>> http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?retmode=text&db=protein&retmax=500&WebEnv=0BUt3HnRet03iYBWkOas0DxsyJKMQliURHWxwJ8fWngZjPLNInSiXg8XrHz@03EE1B259DFC1621_0084SID&rettype=genbank&query_key=1&retstart=0
>>
>> Where WebEnv is set up by the previous query to esearch.fcgi...
>>
>> Currently the first wget is returning s 200+Mb XML file... and it's  
>> not done yet...
>>
>> My choices at this point are basically to either disable sequence  
>> loading for golite (as is for go full), or disable golite loading  
>> altogether until I can figure out what the correct NCBI jiggery- 
>> pokery is.
>>
>> Ben
>> --
>> Ben Hitz
>> Senior Scientific Programmer ** Saccharomyces Genome Database ** GO  
>> Consortium
>> Stanford University ** hitz at genome.stanford.edu
>>
>>
>
> --
> Ben Hitz
> Senior Scientific Programmer
> Saccharomyces Genome Project
> Stanford University
> hitz at genome.stanford.edu
>
>
>
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