[Biopython] NCBIWWW qblast Times Out?

Peter Cock p.j.a.cock at googlemail.com
Wed Apr 25 05:17:16 EDT 2012

On Tue, Apr 24, 2012 at 6:51 PM, Caroline Chang
<carolinechang810 at gmail.com> wrote:
> Hi,
> I'm not sure I'm using the NCBIWWW module correctly. I've followed the example
> code given in the tutorial (
> http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc82) for my own single
> sequence file. However, it seems to hang on the a line of code where it
> sleeps, and then my request times out.
> Is anyone else having this error, or am I using this code incorrectly?
> Thanks!
> Caroline

Hi Caroline,

The most likely cause was the NCBI BLAST service being under heavy load
(especially likely during USA working hours). Did this problem persist, and
has it every worked for you?

If it has never worked for you it could be network problem at your institute
(e.g. some proxy settings).

Another useful check would be to try running the unit test in the Tests
folder of the Biopython source, test_NCBI_qblast.py - and see what
that says.


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