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 <[email protected]> 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 > <[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
