[Bioperl-l] Problem with T-Coffee

[Jonathan Manning]

Hi Jason,

Yes I did; but I eventually gave up and used Muscle
instead which works fine!

Thanks,

Jon

 --- Jason Stajich <jason.stajich at duke.edu> wrote: 
> Did you also symlink mocca and lalign2list in
> addition to t_coffee as 
> those are also depended on by t_coffee?
> 
> -jason
> 
> On Aug 28, 2004, at 1:05 AM, Jonathan Manning wrote:
> 
> > Hi Jason,
> >
> > Thanks for the reply.
> >
> > My versions of Bioperl, Bioperl-run and T-Coffee
> are
> > the same on both machines.
> >
> > When I run the test I get the following output:
> >
> >
> > 1..22
> > # Running under perl version 5.008 for linux
> > # Current time local: Fri Aug 27 10:10:30 2004
> > # Current time GMT:   Fri Aug 27 14:10:30 2004
> > # Using Test.pm version 1.23
> > ok 1
> > ok 2
> > ok 3
> > ok 4
> > ok 5
> >
> > Abnormal Program Termination:[T-COFFEE,
> Version_1.37]
> > Please report the fault to:
> > cedric.notredame at europe.com (Indicate the version
> nu
> > mber)
> > Thank you for your cooperation :-)
> >
> > ------------- EXCEPTION  -------------
> > MSG: TCoffee call crashed: 256 [command
> > /usr/bin/t_coffee -in=t/data/cysprot.fa,
> > Xblosum,Mlalign_id_pair,Mclustalw_pair  -ktuple=3
> > -output=clustalw -outfile=/tmp
> > /MvE0LpuQko/mPn9bfUyI0 -quiet]
> >
> > STACK Bio::Tools::Run::Alignment::TCoffee::_run
> > Bio/Tools/Run/Alignment/TCoffee.
> > pm:814
> > STACK Bio::Tools::Run::Alignment::TCoffee::align
> > Bio/Tools/Run/Alignment/TCoffee
> > .pm:719
> > STACK toplevel t/TCoffee.t:62
> >
> > --------------------------------------
> > ok 6 # skip TCoffee program not found. Skipping.
> >
> > ok 7 # skip TCoffee program not found. Skipping.
> >
> > ok 8 # skip TCoffee program not found. Skipping.
> >
> > ok 9 # skip TCoffee program not found. Skipping.
> >
> > ok 10 # skip TCoffee program not found. Skipping.
> >
> > ok 11 # skip TCoffee program not found. Skipping.
> >
> > ok 12 # skip TCoffee program not found. Skipping.
> >
> > ok 13 # skip TCoffee program not found. Skipping.
> >
> > ok 14 # skip TCoffee program not found. Skipping.
> >
> > ok 15 # skip TCoffee program not found. Skipping.
> >
> > ok 16 # skip TCoffee program not found. Skipping.
> >
> > ok 17 # skip TCoffee program not found. Skipping.
> >
> > ok 18 # skip TCoffee program not found. Skipping.
> >
> > ok 19 # skip TCoffee program not found. Skipping.
> >
> > ok 20 # skip TCoffee program not found. Skipping.
> >
> > ok 21 # skip TCoffee program not found. Skipping.
> >
> > ok 22 # skip TCoffee program not found. Skipping.
> >
> >
> > I guess that explains something- it's not seeing
> the
> > T-Coffee program for some reason. I don't know why
> it
> > shouldn't- I placed it in /usr/bin using a
> soft-link
> > (ln -s).
> >
> > Nothing unusual with my sequence file, but I'm
> > attaching it anyway, and relevant snippet of code
> is
> > below (it's a subroutine passed an arrayref of
> > sequences):
> >
> >  sub align {
> >
> > 	# T-COFFEE USED TO CREATE A Bio::SimpleAlign
> OBJECT
> >
> >     my ($self) = shift;
> >     my ( $relatives, $params ) = @_;
> >     my @params  = @{$params};
> >     my $Aligner = new
> > Bio::Tools::Run::Alignment::TCoffee(@params);
> >     my $aln     = $Aligner->align($relatives);
> >
> >     return $aln;
> > }
> >
> > I don't really have time to swap the program I'm
> > using, so I hope I can get this to work!
> >
> > Thanks again- help appreciated.
> >
> > Jon
> >
> >
> >  --- Jason Stajich <jason at cgt.duhs.duke.edu>
> wrote:
> >> different versions of bioperl/bioperl-run on the
> dev
> >> machine and other
> >> machine?  This happens for every every
> >> alignment you try on the non-dev machine? i.e.
> >> % perl -I. -w t/TCoffee.t
> >> in bioperl-run fails on the new machine too?
> >>
> >> An example sequence file and the script with at
> >> least the t-coffee part
> >> would help in debugging the problem if all of
> that
> >> is true.
> >>
> >> I've also moved to using MUSCLE instead of
> T-Coffee
> >> for some analyses
> >> because it is much faster and seems to be as
> >> accurate.  The newest MAFFT
> >> is also rumoured to be as accurate too although
> one
> >> should always do their
> >> own tests on one's own data first...
> >>
> >> -jason
> >> On Fri, 27 Aug 2004, [iso-8859-1] Jonathan
> Manning
> >> wrote:
> >>
> >>> Hi to all,
> >>>
> >>> I've been using T-Coffee via the Bioperl wrapper
> >> as
> >>> part of a larger project. Though it worked fine
> on
> >> the
> >>> development system, it's not working on a
> >> different
> >>> one. It seems to do the pairwise stuff, at least
> >> it
> >>> gets to this stage:
> >>>
> >>> ......
> >>> 	AAH76853  CAG05593 : score=  400
> >>> 	AAH76853  CAE45989 : score=  410
> >>> 	CAG05593  CAE45989 : score=  460
> >>>
> >>>
> >>> MAKE NEIGHBOR JOINING DENDROGRAM
> >>> 	[MODE=fast] [Output dendrogram
> >> file=5XIMxfCi1F.dnd]
> >>>
> >>>
> >>> But then it crashes out with the following
> >> messages:
> >>>
> >>> Abnormal Program Termination:[T-COFFEE,
> >> Version_1.37]
> >>> Please report the fault to:
> >>> cedric.notredame at europe.com (Indicate the
> version
> >>> number)
> >>> Thank you for your cooperation :-)
> >>>
> >>> ------------- EXCEPTION  -------------
> >>> MSG: TCoffee call crashed: 256 [command
> >>> /usr/bin/t_coffee
> >>>
> >>
> >
>
-in=/tmp/5XIMxfCi1F,XBLOSUM,Mlalign_id_pair,Mclustalw_pair
> >>>  -ktuple=2 -output=clustalw
> >>> -outfile=/tmp/6wIuLkvcGl/w7jE5bLbih]
> 
=== message truncated === 


	
	
		
___________________________________________________________ALL-NEW Yahoo! Messenger - all new features - even more fun!  http://uk.messenger.yahoo.com