Re: [Dart-help] help with windowlicker

[Ian H. <ih...@be...>]

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.
>>  >
>>