[Go] go db issues

[Benjamin Hitz]

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