[Biojava-l] Multiple Sequence Alignment - Limits?

[Hannes Brandstätter-Müller]

I'm currently running another test, now with even more memory for java
(500M) - it looks fine now so far. I'll re-check it later with the
other files that gave me some problems, and will report back later
today.

I had a "out of heap" exception when I tried it with the default
memory settings, and with 256M it seems to have swallowed some
sequences - I'll re-check and help you reproduce. It would be really
bad if the code would swallow sequences without error messages when
running out of memory, so I'll make sure I have proof :D

Hannes

On Wed, Oct 19, 2011 at 09:22, Spencer Bliven <sbliven at ucsd.edu> wrote:
> Hannes–
>
> There should not be a limit on the number of sequences, nor should you be
> running into a memory problem. The FastaParser should be able to read
> thousands of sequences, since it is used for genome FASTA files as well as
> multiple alignments. My guess would be either a malformed FASTA file
> (perhaps a problem with line endings?), or else a problem with the code to
> generate the MultipleAlignment. Can you post some code snippets?
>
> -Spencer
>
> On Tue, Oct 18, 2011 at 21:36, Hannes Brandstätter-Müller
> <biojava at hannes.oib.com> wrote:
>>
>> Hi Andreas,
>>
>> I will try that later today if that makes any difference; I ran a
>> larger alignment batch overnight, and I noticed that this limit seems
>> to have been a coincidence; HOWEVER, the aligned sequences are always
>> not as many as the input sequences, is this caused by memory
>> constraints or how can I influence that?
>>
>> Hannes
>>
>> On Tue, Oct 18, 2011 at 23:01, Andreas Prlic <andreas at sdsc.edu> wrote:
>> > Hi Hannes,
>> >
>> > did you try to increase memory settings for your JVM?  e.g. -Xmx500M
>> >
>> > Andreas
>> >
>> > On Tue, Oct 18, 2011 at 2:46 AM, Hannes Brandstätter-Müller
>> > <biojava at hannes.oib.com> wrote:
>> >> On Tue, Oct 18, 2011 at 11:32, Hannes Brandstätter-Müller
>> >> <biojava at hannes.oib.com> wrote:
>> >>> Hi again!
>> >>>
>> >>> I am quite happy with the Multiple Sequence Alignment, but I noticed
>> >>> that there seems to be a limit of 132 Sequences that are present in
>> >>> the final alignment - is this some kind of hardcoded limit, or can I
>> >>> work around that somehow?
>> >>>
>> >>> Hannes
>> >>>
>> >>
>> >> Sorry, I counted that wrong. I had 132 lines, that is 66 sequences in
>> >> fasta format. Is there a way to work around that limit?
>> >>
>> >> Hannes
>> >>
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>> >>
>> >
>>
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