Re: [Dart-help] help with windowlicker

[marcin j. <mar...@gm...>]

hey,

Thanks for the help!
The short example worked just fine.

log3 with my previous command so far produced this:
Finding eigenvectors using MatrixExpEigenPrepare
Largest eigenvalue was 0; set to 0
Updating cached M() & J()
Finding eigenvectors using MatrixExpEigenPrepare
Largest eigenvalue was 0; set to 0
Setting eigenvalue #2 ((-1.3333,0)) equal to eigenvalue #0 ((-1.3333,0))
Setting eigenvalue #3 ((-1.3333,0)) equal to eigenvalue #0 ((-1.3333,0))
Setting eigenvalue #3 ((-1.3333,0)) equal to eigenvalue #2 ((-1.3333,0))
Updating cached M() & J()
Sequence_database: converting ASCII sequences to score profiles
Processed 3 sequences
Estimating tree for the following sequences: CP000112 CP000527 AE017286
Estimating distances of sequences 0 and 1

You can download the FASTA and Stock files here:
http://www.microbesonline.org/tmp/marcin/DvH_DP4_G20_mVISTA.fasta.gz
http://www.microbesonline.org/tmp/marcin/DvH_DP4_G20_mVISTA.stock.gz

I'll have more updates on Monday -- enjoy the weekend,
marcin
- Show quoted text -

On Sat, Apr 26, 2008 at 1:25 PM, Ian Holmes <ih...@be...> wrote:
> Thanks Marcin.
>
>  Something has definitely gone wrong if no alignment is output. Can you
> check that the following outputs an alignment+tree?
>
>  xrate -log 5 --noannotate -e ~/dart/grammars/jukescantor.eg
> ~/dart/src/ecfg/t/notree.stk
>
>
>  Looking at your log messages it seems like the program has crashed while
> trying to do neighbor-joining to estimate the tree. For the above command, I
> get log messages after the "Estimating tree..." message. See below (BTW many
> of these are on stderr, not stdout)
>
>  If you can reproduce this on the short example pairwise alignment but not
> with the 3M alignments, there's something else wrong that needs
> investigation. In that case, can you first try running "-log 3" instead of
> "-log 5" (this will give more verbose log messages during the
> neighbor-joining algorithm), then mail the stderr log messages to me, and/or
> please post a URL to your large file so I can download it and attempt to
> reproduce the error.
>
>  Sorry about this...
>  Ian
>
>
>
>
>  Warning -- used random number generator during initialisation
>  Read 1 alignments
>  Sequence_database: converting ASCII sequences to score profiles
>  Estimating tree for the following sequences: X Y
>  Optimizing branch lengths of all trees in alignment database, using EM
>  Optimizing tree branch lengths by EM.
>  Tree before optimization:
>  (X:5.0000000000,Y:5.0000000000)root;
>  EM iteration #1: log-likelihood = -56.0101 bits
>  Optimized tree after step #1:
>  (X:5.1160179765,Y:5.1160180140)root;
>  EM iteration #2: log-likelihood = -56.0118 bits
>  Warning: log-likelihood dropped from -56.0101 to -56.0118 bits during EM
>  Failed EM improvement threshold for the 1th time; stopping
>  Checking post-iteration log-likelihood
>  Post-iteration log-likelihood = -56.0118 bits
>  Restoring previous best branch lengths
>  Tree after optimization:
>  (X:5.0000000000,Y:5.0000000000)root;
>  Alignment database log-likelihood: -56.0101 bits
>  Processing alignment Alignment1 (1 of 1): 14 columns
>  # STOCKHOLM 1.0
>  #=GF NH (X:5.0000000000,Y:5.0000000000)root;
>  X       AAAAAAaaUUUUUU
>  Y       GGGGGGaaCCCCCC
>  //
>
>
>
>
>  marcin joachimiak wrote:
>
> > Hey there,
> >
> > The xrate tree job took a while but it seemed to finish without
> > errors. Alas there isn't any tree output ...
> >
> > Here's what I get from stdout:
> >
> > Parsed command line: xrate DvH_DP4_G20_mVISTA.stock -e
> > /usr2/people/gtl/bin/dart//grammars/jukescantor.eg --noannotate -log 5
> > Warning -- used random number generator during initialisation
> > Read 1 alignments
> > Sequence_database: converting ASCII sequences to score profiles
> > Estimating tree for the following sequences: CP000112 CP000527 AE017286
> >
> > The alignment is 3 bacterial genomes, ~3M each -- that wouldn't be a
> > problem right? And this was run on a hefty machine ...
> >
> >
> > marcin
> >
> > On Thu, Apr 24, 2008 at 7:36 PM, marcin joachimiak
> > <mar...@gm...> wrote:
> >
> > > much better, thanks!
> > >  I did notice the trees for each alignment in the output ...
> > >
> > >  The tree estimation is running, I'll keep reporting ...
> > >
> > >
> > >
> > >
> > >  On Thu, Apr 24, 2008 at 7:22 PM, Ian Holmes <ih...@be...> wrote:
> > >  > marcin joachimiak wrote:
> > >  >  > Excellent, its working now!
> > >  >
> > >  >  Cool!
> > >  >
> > >  >
> > >  >  > I'll have the tree data soon and may try a run with as well, but
> best
> > >  >  > if I could know that the other tree is different from the xrate
> one
> > >  >  > with the Jukes-Cantor model. Can I get the Jukes-Cantor model
> > >  >  > tree/distances from xrate?
> > >  >
> > >  >  Yes, it will insert the trees into the alignment files it outputs,
> using
> > >  >  the New-Hampshire-encoded-in-Stockholm format from my previous
> email.
> > >  >
> > >  >  One caveat. The way you're running it now, it is calculating a
> separate
> > >  >  tree *for every window* in the alignment. This may not be what you
> want,
> > >  >  and it's certainly going to slow things down.
> > >  >
> > >  >  If you want to calculate the tree just once for the whole alignment,
> type
> > >  >
> > >  >  xrate MY_ALIGNMENT.stock -e $DARTDIR/grammars/jukescantor.eg
> > >  >  --noannotate -log 5 > MY_ALIGNMENT_WITH_TREE.stock
> > >  >
> > >  >
> > >  >  The "--noannotate" just means "don't waste time trying to annotate
> this
> > >  >  alignment, I just want the tree". The "-log 5" will just print some
> log
> > >  >  messages on stderr, so you can watch the progress of the
> tree-building
> > >  >  algorithms.
> > >  >
> > >  >  hth,
> > >  >
> > >  >  I.
> > >  >
> > >
> > >
> >
>