<div dir="ltr"><div><div><div><div><div><div><div><div><div><div><div>Hi Peter,<br><br></div>It seems that I may have been black-listed, unfortunately. I didn't think it was the case because I've been traveling (and so my IP address has been changing), but when I tried running my program with a VPN, it worked fine again. I'll be more careful.<br><br></div>I am getting an error with the test_NCBI_qblast.py, though:<br><br></div>FAIL: test_orchid_est (__main__.TestQblast)<br>------------------------------------------------------------<br></div>Traceback (most recent call last):<br></div> File "test_NCBI_qblast.py', line 69, in test_orchid_est<br></div> 0.0000001, None, ["21554275", "18409071", "296087288"])<br></div> File "test_NCBI_qblast.py', line 124, in run_qblast<br></div> % ", ".join(expected_hits)<br></div>AssertionError: Missing all of 21554275, 18409071, 296087288 in alignments<br>------------------------------------------------------------<br><br></div>Thank you for your help!<br><br></div>--Lev<br></div><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Jun 22, 2015 at 10:07 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>
Can you run any small tests with Biopython? e.g. test_NCBI_qblast.py<br>
in the Tests folder of the Biopython source code.<br>
<br>
If they also fail, it would be interesting to see the exception message(s).<br>
That might give some clues (e.g. a local network problem).<br>
<br>
My guess is something changed at the NCBI - perhaps they are now<br>
stricter about long running jobs, or if you are very unlucky it might<br>
be that your IP address was (temporarily) black listed for too much<br>
usage?<br>
<span class="HOEnZb"><font color="#888888"><br>
Peter<br>
</font></span><div class="HOEnZb"><div class="h5"><br>
On Mon, Jun 22, 2015 at 3:49 PM, Lev Tsypin <<a href="mailto:ltsypin@uchicago.edu">ltsypin@uchicago.edu</a>> wrote:<br>
> Hi Peter,<br>
><br>
> Unfortunately, I think that might not be an option for me. The software I'm<br>
> trying to write is meant to be an open-source tool that researchers would<br>
> just be able to use without extensive set up required. I'm afraid that I<br>
> won't be able to ask people to install standalone BLAST and learn to use<br>
> computer clusters, without losing the accessibility of the program.<br>
><br>
> Do you think that this is really the BLAST server being busy? As I said, I<br>
> didn't have any problems for a long time. The average time to get a BLAST<br>
> result back would be about 6-7 minutes. Now I just don't get through.<br>
><br>
> Best,<br>
> Lev<br>
><br>
> On Mon, Jun 22, 2015 at 4:03 AM, Peter Cock <<a href="mailto:p.j.a.cock@googlemail.com">p.j.a.cock@googlemail.com</a>><br>
> wrote:<br>
>><br>
>> 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>
>><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<br>
>> > 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,<br>
>> > though,<br>
>> > and I am not quite sure how to explain it, or respond to it, so I wanted<br>
>> > 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<br>
>> > cases<br>
>> > that it would get stuck for a long time (up to an hour or so), but it<br>
>> > would<br>
>> > then manage to fight through whatever obstacle and go on. In such cases,<br>
>> > I<br>
>> > also found that if I were to artificially restart the request, the<br>
>> > function<br>
>> > would rouse itself and go much better. Here's an example of a function<br>
>> > call:<br>
>> ><br>
>> > blastp_result = NCBIWWW.qblast('blastp', 'nr',<br>
>> ><br>
>> > 'MSLSREENIYMGKISEQTERFEDMLEYMKKVVQTGQELSVEERNLLSVAYKNTVGSRRSAWRSISAIQQKEESKGSKHLDLLTNYKKKIETELNLYCEDILRLLNDYLIKNATNAEAQVFFLKMKGDYYRYIAEYAQGDDHKKAADGALDSYNKASEIANSELSTTHPIRLGLALNFSVFHYEVLNDPSKACTLAKTAFDEAIGDIERIQEDQYKDATTIMQLIRDNLTLWTSEFQDDAEEQQE',<br>
>> > entrez_query = 'NOT Ciliata').read()<br>
>> ><br>
>> > [In the protein sequence above I have multiple lines so that it fits in<br>
>> > 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<br>
>> > stuck<br>
>> > for so long, and what should I do now that it never seems to work<br>
>> > 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<br>
>> > automatically<br>
>> > retry? I know there is an optional parameter in the urllib2 library for<br>
>> > a<br>
>> > time out, but, looking at the source code for NCBIWWW.qblast(), it<br>
>> > 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>
>> > _______________________________________________<br>
>> > Biopython-dev mailing list<br>
>> > <a href="mailto:Biopython-dev@mailman.open-bio.org">Biopython-dev@mailman.open-bio.org</a><br>
>> > <a href="http://mailman.open-bio.org/mailman/listinfo/biopython-dev" rel="noreferrer" target="_blank">http://mailman.open-bio.org/mailman/listinfo/biopython-dev</a><br>
><br>
><br>
</div></div></blockquote></div><br></div>