Hi Hannes, just did a MSA test with 521 seq... and it works. It must be a memory issue.
try something like: java -Xmx1g -jar yourApp.jar args... If you don't have enough RAM, try with 500m as suggested by Andreas, Regards, Khalil On 19 Oct 2011, at 18:00, [email protected] wrote: > Send Biojava-l mailing list submissions to > [email protected] > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.open-bio.org/mailman/listinfo/biojava-l > or, via email, send a message with subject or body 'help' to > [email protected] > > You can reach the person managing the list at > [email protected] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Biojava-l digest..." > > > Today's Topics: > > 1. Re: Multiple Sequence Alignment - Limits? (Andreas Prlic) > 2. Re: Multiple Sequence Alignment - Limits? > (Hannes Brandst?tter-M?ller) > 3. Re: Multiple Sequence Alignment - Limits? > (Hannes Brandst?tter-M?ller) > 4. Re: Multiple Sequence Alignment - Limits? (Spencer Bliven) > 5. Status of org.biojava3.data.sequence.SequenceUtil ? > ([email protected]) > 6. Re: Status of org.biojava3.data.sequence.SequenceUtil ? > (Peter Troshin) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 18 Oct 2011 14:01:05 -0700 > From: Andreas Prlic <[email protected]> > Subject: Re: [Biojava-l] Multiple Sequence Alignment - Limits? > To: Hannes Brandst?tter-M?ller <[email protected]> > Cc: biojava-l <[email protected]> > Message-ID: > <calthepz+7+ko1jo5gfiyhtj-27jojgahje7d55-b0shuazd...@mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > 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 Brandst?tter-M?ller > <[email protected]> wrote: >> On Tue, Oct 18, 2011 at 11:32, Hannes Brandst?tter-M?ller >> <[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 >> > > > > ------------------------------ > > Message: 2 > Date: Wed, 19 Oct 2011 06:36:19 +0200 > From: Hannes Brandst?tter-M?ller <[email protected]> > Subject: Re: [Biojava-l] Multiple Sequence Alignment - Limits? > To: Andreas Prlic <[email protected]> > Cc: biojava-l <[email protected]> > Message-ID: > <CAPXi2mkBsBJhzfHKtgquytXPV=hF0TZNYAM8cfCcen=qfma...@mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > 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 Brandst?tter-M?ller >> <[email protected]> wrote: >>> On Tue, Oct 18, 2011 at 11:32, Hannes Brandst?tter-M?ller >>> <[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 >>> >> > > > > ------------------------------ > > Message: 3 > Date: Wed, 19 Oct 2011 09:32:25 +0200 > From: Hannes Brandst?tter-M?ller <[email protected]> > Subject: Re: [Biojava-l] Multiple Sequence Alignment - Limits? > To: Spencer Bliven <[email protected]> > Cc: biojava-l <[email protected]> > Message-ID: > <CAPXi2mnzkvLasRWixinxyh=w=v6bjepxrphtygf54ac5dfn...@mail.gmail.com> > Content-Type: text/plain; charset=windows-1252 > > 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 Brandst?tter-M?ller >> <[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 Brandst?tter-M?ller >>>> <[email protected]> wrote: >>>>> On Tue, Oct 18, 2011 at 11:32, Hannes Brandst?tter-M?ller >>>>> <[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 >> >> > > > > ------------------------------ > > Message: 4 > Date: Wed, 19 Oct 2011 00:22:55 -0700 > From: Spencer Bliven <[email protected]> > Subject: Re: [Biojava-l] Multiple Sequence Alignment - Limits? > To: Hannes Brandst?tter-M?ller <[email protected]> > Cc: biojava-l <[email protected]> > Message-ID: > <CA+P6arns8F9XeZj4UK0hEmvV_uOG5nJxoZxJ5fBQ=ndh-xu...@mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > 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 Brandst?tter-M?ller < > [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 Brandst?tter-M?ller >>> <[email protected]> wrote: >>>> On Tue, Oct 18, 2011 at 11:32, Hannes Brandst?tter-M?ller >>>> <[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 >> > > > > ------------------------------ > > Message: 5 > Date: 19 Oct 2011 12:15:26 +0100 > From: [email protected] > Subject: [Biojava-l] Status of org.biojava3.data.sequence.SequenceUtil > ? > To: biojava-l <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; format=flowed; charset=ISO-8859-1 > > Hello, > > I can't find a jar containing org.biojava3.data.sequence.SequenceUtil, even > though it appears in the JavaDocs: > http://www.biojava.org/docs/api/org/biojava3/data/sequence/SequenceUtil.html > > What is it's status? Can I get it, and should it rely on it if I can? > > Thanks, > > Jon > > > > > ------------------------------ > > Message: 6 > Date: Wed, 19 Oct 2011 16:13:44 +0100 > From: Peter Troshin <[email protected]> > Subject: Re: [Biojava-l] Status of > org.biojava3.data.sequence.SequenceUtil ? > To: [email protected] > Cc: [email protected] > Message-ID: <[email protected]> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Jon, > > This class is a part of protein disorder prediction JAR and a recent > addition to BioJava. You are welcome to use if it suits your needs. > Bear in mid though that the FASTA file reader from this class reads the > content of the whole FASTA file at once, i.e. if you are working with > large FASTA files you will want to use something else instead. I've got > a Stream based FASTA reader if you need one and if there is not one in > BioJava already. > I would imagine the functionality from this class is not going to > disappear overnight, but it may and perhaps should be merged with other > FASTA parsers in BioJava once somebody have time to do this. > > Regards, > Peter > > > On 19/10/2011 12:15, [email protected] wrote: >> Hello, >> >> I can't find a jar containing org.biojava3.data.sequence.SequenceUtil, >> even though it appears in the JavaDocs: >> http://www.biojava.org/docs/api/org/biojava3/data/sequence/SequenceUtil.html >> >> What is it's status? Can I get it, and should it rely on it if I can? >> >> Thanks, >> >> Jon >> >> >> _______________________________________________ >> 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 > > > End of Biojava-l Digest, Vol 105, Issue 12 > ****************************************** _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
