Re: [Dart-help] help with windowlicker

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

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 )

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
>