Re: [Dart-help] help with windowlicker

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

marcin joachimiak wrote:
> Thanks!
> Initially the only environment changes I made was adding the perl
> module dir to PERLLIB.
> 
> I've now created the DARTDIR variable and there is some progress but
> now I get a different error message:
> 
> -bash-3.00$  perl /usr2/people/gtl/bin/dart/perl/windowlicker.pl
> DvH_DP4_G20_mVISTA.stock
> [stderr] ERROR: Every input alignment needs to be annotated with a
> phylogenetic tree.
> [stderr] Given that this isn't the case, I need a rate matrix in order
> to do some ad-hoc phylogeny
> [stderr]  (neighbor-joining followed by EM on the branch lengths, if
> you must know.)
> [stderr] I want to get that rate matrix from the tree estimation grammar file.
> [stderr] However, I haven't been told about any such file, so I'm bailing.
> xrate returned with nonzero exit status (invoked using:
> /usr2/people/gtl/bin/dart//bin/xrate )

Do you already have a phylogenetic tree for these sequences? If so, and
you can write the tree in New Hampshire format, then you can put it
directly into your Stockholm alignment file, like so:

# STOCKHOLM 1.0
#=GF NH ((seq1:0.01,seq2:0.03):0.04,seq3:0.05);
seq1 AAGGGCCC
seq2 AGGGGCCT
seq3 GAGGGCCT
//


If not, you need to specify a grammar file for tree estimation. This is
not the same as the grammar file for alignment annotation (confusing, I
know). Currently tree estimation can only be done with simpler grammars
than the RNA gene prediction model we are using.

We typically use the Jukes-Cantor model for tree estimation. This is
encoded as a grammar file in "$DARTDIR/grammars/jukescantor.eg". To
specify the tree-estimation grammar, you use the "-e" option (the "-g"
option is for the alignment annotation grammar).

So, what you want is probably something like this:

perl /usr2/people/gtl/bin/dart/perl/windowlicker.pl
DvH_DP4_G20_mVISTA.stock -- -e $DARTDIR/grammars/jukescantor.eg


hope this helps! if not, send along the alignment file and I'll take a look.

Ian




> 
> I've also tried specifying the grammer file for xrate but apparently
> unsuccessfully:
> 
> -bash-3.00$  perl /usr2/people/gtl/bin/dart/perl/windowlicker.pl
> DvH_DP4_G20_mVISTA.stock -- -g ncRna_v22.eg
> [stderr] ERROR: Every input alignment needs to be annotated with a
> phylogenetic tree.
> [stderr] Given that this isn't the case, I need a rate matrix in order
> to do some ad-hoc phylogeny
> [stderr]  (neighbor-joining followed by EM on the branch lengths, if
> you must know.)
> [stderr] I want to get that rate matrix from the tree estimation grammar file.
> [stderr] However, I haven't been told about any such file, so I'm bailing.
> xrate returned with nonzero exit status (invoked using:
> /usr2/people/gtl/bin/dart//bin/xrate -g ncRna_v22.eg)
> 
> 
> marcin
> 
> 
> 
> On Thu, Apr 24, 2008 at 5:07 PM, Ian Holmes <ih...@be...> wrote:
>> Hi Marcin,
>>
>>  first, sorry I didn't reply to your earlier email to me, been a bit busy
>>  here. There is actually a dart-help mailing list...
>>
>>  http://biowiki.org/DartMailingLists
>>
>>  ...but it'll pretty much end up in the same inboxes if you email
>>  holmes-lab instead ;)
>>
>>
>>  second, the error you're getting means that xrate couldn't be run. If
>>  you just type "xrate -h" from your command prompt, do you get a help
>>  message? Or do you have to type in the entire path to xrate, e.g.
>>  "/nfs/src/dart/bin/xrate -h" or whatever?
>>
>>  If the latter, then it's likely that windowlicker just can't find the
>>  xrate binary. You can test this by typing "windowlicker.pl -h" and
>>  looking at the "-x" option, whose default value is the path that
>>  windowlicker is trying to use.
>>
>>  Best fix for this is to set the DARTDIR environment variable to the root
>>  of your DART installation (/nfs/src/dart in the above example). You can
>>  also use windowlicker's -x option to tell it the path to the xrate
>>  executable.
>>
>>
>>  third, if the above doesn't fix your problem, can you email me the
>>  actual file you're having problems with (if it's huge, then gzip or bzip
>>  it first) so I can try to reproduce the issue.
>>
>>
>>  Hope this helps!
>>  Ian
>>
>>
>>
>>  PS I am still trying to get around to reading your guide tree
>>  manuscript. It will happen though!
>>
>>
>>
>>
>>  marcin joachimiak wrote:
>>  > hello,
>>  >
>>  > I have the DART package built and running at the syntax help level.
>>  > Formatting the FASTA file to Stockholm was successful.
>>  > I've tried running windowlicker on the stocholm data and got:
>>  >
>>  > -bash-3.00$ perl /usr2/people/gtl/bin/dart/perl/windowlicker.pl
>>  > DvH_DP4_G20_mVISTA.stock
>>  > xrate failed (check command-line options? they were: xrate )
>>  >
>>  > So I assume there are more required arguments? And how would I supply
>>  > the reference grammars?
>>  >
>>  > thanks,
>>  > marcin
>>