<div dir="ltr"><div><div>Hi Peter,<br><br></div>Unfortunately, I think that might not be an option for me. The software I'm trying to write is meant to be an open-source tool that researchers would just be able to use without extensive set up required. I'm afraid that I won't be able to ask people to install standalone BLAST and learn to use computer clusters, without losing the accessibility of the program.<br><br></div><div>Do you think that this is really the BLAST server being busy? As I said, I didn't have any problems for a long time. The average time to get a BLAST result back would be about 6-7 minutes. Now I just don't get through.<br><br></div><div>Best,<br></div><div>Lev<br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Jun 22, 2015 at 4:03 AM, Peter Cock <span dir="ltr"><<a href="mailto:p.j.a.cock@googlemail.com" target="_blank">p.j.a.cock@googlemail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Lev,<br>
<br>
My usual advice when dealing with any large-scale BLAST<br>
search is to download the NCBI database and use standalone<br>
BLAST+ locally, rather than the NCBI web-service which<br>
can be busy - especially during USA working hours.<br>
<br>
Do you have access to a local Linux cluster or similar? It is<br>
very likely there are people in your department/university<br>
already doing this - often the SysAdmin will keep a single<br>
shared copy of the databases up to date for everyone to<br>
use.<br>
<br>
(You would likely need to do some post-filtering to remove<br>
any Ciliata hits since the Entrez query option is only available<br>
when running BLAST at the NCBI.)<br>
<br>
Peter<br>
<div><div class="h5"><br>
On Sun, Jun 21, 2015 at 7:19 PM, Lev Tsypin <<a href="mailto:ltsypin@uchicago.edu">ltsypin@uchicago.edu</a>> wrote:<br>
> Hello everyone,<br>
><br>
> I have been writing a tool that makes use of Biopython for automatic BLAST<br>
> searches--your libraries have made my life so much easier! I really<br>
> appreciate your work. I've recently begun to run into some trouble, though,<br>
> and I am not quite sure how to explain it, or respond to it, so I wanted to<br>
> ask for advice:<br>
><br>
> The issue is that, of late, when I call the NCBIWWW.qblast function, it<br>
> takes forever--literally never finishing. Before, there were sometimes cases<br>
> that it would get stuck for a long time (up to an hour or so), but it would<br>
> then manage to fight through whatever obstacle and go on. In such cases, I<br>
> also found that if I were to artificially restart the request, the function<br>
> would rouse itself and go much better. Here's an example of a function call:<br>
><br>
> blastp_result = NCBIWWW.qblast('blastp', 'nr',<br>
> 'MSLSREENIYMGKISEQTERFEDMLEYMKKVVQTGQELSVEERNLLSVAYKNTVGSRRSAWRSISAIQQKEESKGSKHLDLLTNYKKKIETELNLYCEDILRLLNDYLIKNATNAEAQVFFLKMKGDYYRYIAEYAQGDDHKKAADGALDSYNKASEIANSELSTTHPIRLGLALNFSVFHYEVLNDPSKACTLAKTAFDEAIGDIERIQEDQYKDATTIMQLIRDNLTLWTSEFQDDAEEQQE',<br>
> entrez_query = 'NOT Ciliata').read()<br>
><br>
> [In the protein sequence above I have multiple lines so that it fits in the<br>
> email, but when I normally run the function I don't have any newline<br>
> characters or anything, of course]<br>
><br>
> My questions are the following: Why does the function sometimes get stuck<br>
> for so long, and what should I do now that it never seems to work anymore?<br>
> Do you have any suggestions for introducing a 'time out' so that if, for<br>
> example, the request takes longer than 10 minutes, it would automatically<br>
> retry? I know there is an optional parameter in the urllib2 library for a<br>
> time out, but, looking at the source code for NCBIWWW.qblast(), it wasn't<br>
> obvious to me whether and how it would work to use it.<br>
><br>
> Thank you very much for any advice.<br>
><br>
> Best regards,<br>
> Lev<br>
><br>
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