[Bioperl-l] Possible problems with file output?

Jonathan Manning jon_r_manning at yahoo.com
Sat Aug 28 12:21:51 EDT 2004

Hi to all,

I've been developing a large bit of perl-based
software which calls on many Bioperl modules. I've
just moved it from the development system to a new
one, and am having some trouble. 

I e-mailed yesterday concerning a problem I was having
with T-Coffee (which I solved by switching to Muscle-
thanks Jason), but am now having a problem with the
Phylip suite this line in the SeqBoot module (359): 

my $outfile =
    $self->throw("SeqBoot did not create files
correctly ($outfile)")
        unless (-e $outfile);

It was at a very similar part in the T-Coffee module
the program crashed out before, from which I infer
that there may be some problems with writing to files
(the programs work fine by themselves). This is not an
issue with file permissions, but I thought maybe I
could be short a module or two necessary for this sort
of thing. Could anyone suggest which ones these might



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