[Bioperl-l] remoteblast xml problem

Sat Jun 3 00:57:37 UTC 2006

Yes, I see the same error you do.  But I have a similar script  
(blastp, XML blast report, XML parsing, similar loop structure) that  
works fine.  I'm trying to dissect the problem but I think it may be  
something logically wrong here (something not so obvious) and not a  
bug...

What I'm trying to say is, when you send sequences using remoteblast  
like, this you are essentially spamming the NCBI BLAST server with  
~1600 requests.  This script wasn't set up with that intent in mind;  
you should really try to set up your own local blast database if  
possible.  If you can't, try running this script in off-hours  
(10pm-6am EST or something like that).

Chris

On Jun 2, 2006, at 7:49 PM, Hubert Prielinger wrote:

> hi,
> input database: swissprot
>         matrix: pam30
>         count: 1
>         gapcosts: 9 1
>
> I know that there are  a lot of sequences, but that doesn't matter,  
> you can delete all of them except one, the amount of the sequences  
> is not the problem, the script reads one line and submits  
> it.....then the second line and so on.....I have tried it with only  
> one sequence either and I got the same result.... the script run at  
> that time for more than 20 minutes!!!!!! .....and that should be  
> enough time to retrieve the results for ONE sequence, I guess
>
> regards
> Hubert
>
>
>
> Chris Fields wrote:
>> You need to add the input conditions as well (you have several  
>> <STDIN> lines which may play a role; I would like to know what you  
>> normally enter for those).
>>
>> How long did you let the script run?  I ran a quick check on your  
>> sequences; you have almost 1600, so you have to expect that you'll  
>> run into some problems here!  Most here (including me) would  
>> suggest you try installing a local blast setup for something like  
>> this.
>>
>> Chris
>>
>> On Jun 2, 2006, at 6:19 PM, Hubert Prielinger wrote:
>>
>>> hi,
>>> I have submitted the bug -> Bug 2017
>>> with the script and input file, just start it from command line
>>>
>>> thank you very much
>>> greetings
>>>
>>> Hubert
>>>
>>> Chris Fields wrote:
>>>> Hubert,
>>>>
>>>> I have a script that's using blastxml and XML output which seems  
>>>> to work.
>>>> I'll try looking at it to get a better idea this weekend.
>>>>
>>>> Chris
>>>>
>>>>
>>>>> -----Original Message-----
>>>>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
>>>>> bounces at lists.open-bio.org] On Behalf Of Hubert Prielinger
>>>>> Sent: Friday, June 02, 2006 4:12 PM
>>>>> To: Chris Fields; bioperl-l at bioperl.org; Chris Fields; 'Sendu  
>>>>> Bala'
>>>>> Subject: Re: [Bioperl-l] remoteblast xml problem
>>>>>
>>>>> hi,
>>>>> sorry, but I have updated the remoteblast module and I have run  
>>>>> several
>>>>> attempts with the same results as before. It didn't work.
>>>>> I didn't get any results.
>>>>>
>>>>> regards
>>>>> Hubert
>>>>>
>>>>>
>>>>> Chris Fields wrote:
>>>>>
>>>>>> Sendu, Hubert,
>>>>>>
>>>>>>
>>>>>> Hubert, your code looks fine so Sendu's patch should fix the  
>>>>>> problem
>>>>>>
>>>>> (break
>>>>>
>>>>>> out of that infinite loop).  I applied Sendu's patch to  
>>>>>> RemoteBlast in
>>>>>>
>>>>> CVS;
>>>>>
>>>>>> it passed all tests in RemoteBlast.t.  Try updating from CVS  
>>>>>> to see if
>>>>>>
>>>>> it
>>>>>
>>>>>> works.
>>>>>>
>>>>>> Chris
>>>>>>
>>>>>>
>>>>>>
>>>>>>> -----Original Message-----
>>>>>>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
>>>>>>> bounces at lists.open-bio.org] On Behalf Of Sendu Bala
>>>>>>> Sent: Friday, June 02, 2006 4:04 AM
>>>>>>> To: bioperl-l at lists.open-bio.org
>>>>>>> Subject: Re: [Bioperl-l] remoteblast xml problem
>>>>>>>
>>>>>>> Hubert Prielinger wrote:
>>>>>>>
>>>>>>>
>>>>>>>> hi,
>>>>>>>> I have the following program and it worked quite well, for  
>>>>>>>> retrieving
>>>>>>>> remoteblast results in a textfile,
>>>>>>>> now I have altered it to to xml, and it didn't work  
>>>>>>>> anymore.....
>>>>>>>> it takes all the parameter at the commandline, submits the  
>>>>>>>> query, but
>>>>>>>>
>>>>> I
>>>>>
>>>>>>>> don't retrieve any results file anymore.....
>>>>>>>>
>>>>>>>> it seems that it hangs in a endless loop......
>>>>>>>> the only output I get is:  $rc is not a ref! over and  
>>>>>>>> over..... it
>>>>>>>> doesn't enter the else term anymore....
>>>>>>>>
>>>>>>>>
>>>>>>> There is no problem with your code. The problem is with the  
>>>>>>> NCBI server
>>>>>>> and should be reported to them. You can visit the site and do  
>>>>>>> a blast,
>>>>>>> requesting xml format, and you will typically get one normal  
>>>>>>> 'waiting'
>>>>>>> message and the promise that it will be updated in x seconds,  
>>>>>>> but
>>>>>>> subsequent attempts to get progress information result in an  
>>>>>>> xml error
>>>>>>> page because the NCBI server doesn't actually send any data.
>>>>>>>
>>>>>>> Unfortunately the way that the bioperl code is written, it  
>>>>>>> treats no
>>>>>>> data as 'waiting' instead of an error. I've offered a patch  
>>>>>>> to fix this
>>>>>>> at this bug page:
>>>>>>> http://bugzilla.bioperl.org/show_bug.cgi?id=2015
>>>>>>> _______________________________________________
>>>>>>> Bioperl-l mailing list
>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>>
>>>>>>>
>>>>>> _______________________________________________
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>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>> _______________________________________________
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>>>>>
>>>>
>>>>
>>>>
>>>
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>>
>> Christopher Fields
>> Postdoctoral Researcher
>> Lab of Dr. Robert Switzer
>> Dept of Biochemistry
>> University of Illinois Urbana-Champaign
>>
>>
>>
>>
>

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign