[Bioperl-l] StandAloneBlast->blastall array of Bio::Seq objects

Chris Fields cjfields at uiuc.edu
Thu Dec 14 13:36:09 EST 2006


On Dec 14, 2006, at 11:49 AM, Andrew Stewart wrote:

>> So can you look at the tempfile that is created and see if it is  
>> sane?
>>
>> Set -save_tempfiles => 1 whene you initialize the factory object  
>> or do
>> $factory->save_tempfiles(1)
>> before calling the blastall.
>>
>> -jason
>>
>
> Jason,
> I was actually wondering how to do that.  Thanks.  Odd though, it
> still doesn't seem to be saving the tempfiles.  Might not matter

That needs to be checked out.  Can anyone verify that?

>> The error pops up when the executable returns a bad status, so
>> maybe it's choking on too many input sequences (i.e. Bioperl is
>> doing everything correctly, but you are attempting to BLAST too
>> many sequences in one go).  How many sequences are you attempting
>> to use as input?  What happens when you use fewer input sequences?
>>
>> chris
>>
>
> I was processing 738 sequences for input.  I cut that down to 20
> sequences and I'm getting some other exception thrown further
> downstream, so it appears you may be correct.  You don't happen to
> know what the max number of sequences that blastall allows for input,
> would ya? ;)  I suppose I'll have to break @query down into smaller
> doses or something.
>
> Thanks,
> Andrew

It was a shot in the dark, really.  The fact that the return status  
was bad could be due to a number of problems (permissions issues, bad  
data, etc).  The fact that a single sequence worked indicated that  
permissions and output format likely weren't to blame.  The only  
other thing left was a problem with blastall itself.

BTW, the blast docs do not indicate whether there is a maximum number  
of sequences.  There may be a point where available memory becomes  
the limiting issue.

chris



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