[Bioperl-l] StandAloneBlast->blastall array of Bio::Seq objects
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
>> Set -save_tempfiles => 1 whene you initialize the factory object
>> or do
>> before calling the blastall.
> 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?
> 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.
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.
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