[Bioperl-l] RemoteBlast by Bio::Perl Through proxy
Madeleine Lemieux
mlemieux at bioinfo.ca
Thu Apr 14 11:46:16 EDT 2005
Chandan,
I don't think your proxy is the problem. Blast_sequence correctly posts
the request but your server's timeout is too short for the NCBI server
to respond. If you compare the number of hops from you to the EBI
server versus you to the NCBI server, I bet the latter is longer. Or
the NCBI's server is just busier and slower to respond.
I've tested going through proxies that either require authentication or
don't. In both cases blast_sequence worked fine.
I don't know enough about how to change the timeout settings to help
you with that but that is where I would look.
Good luck,
Madeleine
> Hi to all
> I found a reason because of which get_sequence works and
> blast_sequence does not .
> The fact is that for "Bio::Perl::blast_sequence " the subroutine
> LWP::UserAgent::env_proxy() is not called while for
> Bio::Perl::get_sequence
> it is called and so Bio::Perl::get_sequence works fine .
> I have run two more programs and am 100% sure of what i'm talking
> about .
> I will be very thankful if somebody could help me out .
> Thanks in advance .
> Chandan
>
> On 4/14/05, CHANDAN SINGH <chandan.kr.singh at gmail.com> wrote:
>> Hi all
>> As already mentioned i get error 500 while using Remoteblast through
>> Bio::Perl module .Most of the time the error is
>> 500 Can't connect to www.ncbi.nlm.nih.gov:80 (connect: No route to
>> host)
>> Sometimes the error is
>> 500 Can't connect to www.ncbi.nlm.nih.gov:80 (connect: timeout)
>> (refer to my first mail for details )
>>
>> Of late I have been trying to trace out the bug and found that
>> The subroutine UserAgent ::_need_proxy returns an undef
>> value
>> in my case .
>> I would like to know more about this subroutine and request all who
>> know about it to please respond .
>> Thanks
>> Chandan
>>
>> On 4/13/05, Madeleine Lemieux <mlemieux at bioinfo.ca> wrote:
>>> Chandan,
>>>
>>> In your own best interest, you should post your responses to the
>>> list.
>>> That way you get the benefit of a large talent pool rather than
>>> limiting yourself to what little I know.
>>>
>>> You can try getting a fresh copy of RemoteBlast.pm from the bioperl
>>> website just in case you unintentionally changed something other than
>>> that one line.
>>>
>>> But it seems to me as if you're timing out before the NCBI server has
>>> time to respond in which case I'm afraid I don't know how to help
>>> you.
>>> If you do traceroute www.ncbi.nlm.nih.gov, do you reach the server
>>> in a
>>> reasonable amount of time?
>>>
>>> Madeleine
>>>
>>>> hi Madeleine Lemieux
>>>> Thanks for ur reply . Yes the error happens everytime i run the
>>>> code
>>>> and you deduced correctly that the get_sequence works
>>>> fine . Yes i did try to appened one line to RemoteBlast after making
>>>> a few attempts to run the code but it did not work and i removed it
>>>> .
>>>> Do you suggest installing the modules again ?
>>>>
>>>> chandan
>>>>
>>>> On Apr 12, 2005 3:55 AM, Madeleine Lemieux <mlemieux at bioinfo.ca>
>>>> wrote:
>>>>> Chandan,
>>>>>
>>>>> Does this error happen every time you run the code? The
>>>>> get_sequence
>>>>> works otherwise your error message would have come from EBI, not
>>>>> NCBI,
>>>>> which means your proxy is set up OK. Both get_sequence and
>>>>> blast_sequence eventually call the same User Agent code so if one
>>>>> works, the other should as well. Have you edited either Perl.pm or
>>>>> RemoteBlast.pm?
>>>>>
>>>>> Madeleine
>>>>>
>>>>>> I am a newbie and while installing bioperl and other related
>>>>>> softwres
>>>>>> i had installation problems
>>>>>> but fortunately succeeded in debugging few .I had no idea where to
>>>>>> share those experiences
>>>>>> but now being a member of this forum might help. Though i dont
>>>>>> have
>>>>>> the installation outputs
>>>>>> i would like to share the last such experience while installind
>>>>>> Berkeley DB .It was not able to include a file Extern.h and i
>>>>>> found
>>>>>> that the concerned file in
>>>>>> /usr/lib/perl5/..../Core/Extern had a wrong extension . After
>>>>>> setting
>>>>>> it to Extern.h installation was
>>>>>> possible.I could not install few other related softwares .
>>>>>>
>>>>>> At present i am facing this problem.The second code for blast in
>>>>>> bptutorial(html format on bioperl site ) when run does not yield
>>>>>> the
>>>>>> desired result .
>>>>>> #! /usr/bin/perl
>>>>>> use Bio::Perl;
>>>>>> $seq_object = get_sequence('swiss',"ROA1_HUMAN");
>>>>>> # uses the default database - nr in this case
>>>>>> $blast_result = blast_sequence($seq_object);
>>>>>>
>>>>>> write_blast(">roa1.blast",$blast_result);
>>>>>> The output after running the code is
>>>>>> ------------------- WARNING ---------------------
>>>>>> MSG: req was POST http://www.ncbi.nlm.nih.gov/blast/Blast.cgi
>>>>>> User-Agent: bioperl-Bio_Tools_Run_RemoteBlast/1.5
>>>>>> Content-Length: 651
>>>>>> Content-Type: application/x-www-form-urlencoded
>>>>>>
>>>>>> DATABASE=nr&QUERY=%3EROA1_HUMAN+Heterogeneous+nuclear+ribonucleopr
>>>>>> ote
>>>>>> in
>>>>>> +A1+(Helix-destabilizing+protein)+(Single-
>>>>>> strand+binding+protein)+(hnRNP+core+protein+A1).%0ASKSESPKEPEQLRKL
>>>>>> FIG
>>>>>> GL
>>>>>> SFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPK
>>>>>> RAV
>>>>>> SR
>>>>>> EDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDS
>>>>>> VDK
>>>>>> IV
>>>>>> IQKYHTVNGHNCEVRKALSKQEMASASSSQRGRSGSGNFGGGRGGGFGGNDNFGRGGNFSGRGGFG
>>>>>> GSR
>>>>>> GG
>>>>>> GGYGGSGDGYNGFGNDGGYGGGGPGYSGGSRGYGSGGQGYGNQGSGYGGSGSYDSYNNGGGRGFGG
>>>>>> GSG
>>>>>> SN
>>>>>> FGGGGSYNDFGNYNNQSSNFGPMKGGNFGGRSSGPYGGGGQYFAKPRNQGGYGGSSSSSSYGSGRR
>>>>>> F&C
>>>>>> OM
>>>>>> POSITION_BASED_STATISTICS=off&EXPECT=1e
>>>>>> -10&SERVICE=plain&FORMAT_OBJECT=Alignment&CMD=Put&FILTER=L&PROGRAM
>>>>>> =bl
>>>>>> as
>>>>>> tp
>>>>>>
>>>>>> <HTML>
>>>>>> <HEAD><TITLE>An Error Occurred</TITLE></HEAD>
>>>>>> <BODY>
>>>>>> <H1>An Error Occurred</H1>
>>>>>> 500 Can't connect to www.ncbi.nlm.nih.gov:80 (connect: No route to
>>>>>> host)
>>>>>> </BODY>
>>>>>> </HTML>
>>>>>>
>>>>>> ---------------------------------------------------
>>>>>> Submitted Blast for [ROA1_HUMAN]
>>>>>>
>>>>>>
>>>>>> The env variable HTTP_PROXY or /and http_proxy is set correct .I
>>>>>> hope
>>>>>> somebody can
>>>>>> help me out .
>>>>>> Thank You .
>>>>>
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at portal.open-bio.org
>>>>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>>>>>
>>>>
>>>
>>>
>>
>
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