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 < [email protected]> 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 <[email protected]> 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 > > <[email protected]> wrote: > >> On Tue, Oct 18, 2011 at 11:32, Hannes Brandstätter-Müller > >> <[email protected]> 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 > >> > >> _______________________________________________ > >> Biojava-l mailing list - [email protected] > >> http://lists.open-bio.org/mailman/listinfo/biojava-l > >> > > > > _______________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
