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--></style><title>what am I doing wrong with
$alignio->next_aln</title></head><body>
<div><font face="Courier New">I'm trying to run PAML through BioPerl.
I get this error message</font></div>
<div><font face="Courier New"><br></font></div>
<div><font face="Courier New">-------------------- WARNING
---------------------<br>
MSG: must have supplied a valid alignment file in order to run
codeml<br>
---------------------------------------------------</font><br>
<font face="Courier New"></font></div>
<div><font face="Courier New">because I'm not getting a return value
from "my $aln = $alignio->next_aln". I just can't
quite figure out why. Here's the code bit. Any help would
be greatly appreciated. I have a feeling this has to do with the
input file, but the format of the file is fine. Is there
something about the path that I'm missing?</font></div>
<div><font face="Courier New"><br></font></div>
<div><font face="Courier New"><br></font></div>
<div><font face="Courier New">if($sepfiles[$x] =~ /.fa$/){<br>
<x-tab> </x-tab>my $tempfile =
'./tempfiles/'.$sepfiles[$x];<br>
<x-tab> </x-tab>print "Datafile is -
$allfiles[$a], $tempfile\n";<br>
<x-tab> </x-tab>##my $tempfile=
shift @ARGV; ## to load infile on command line<br>
<x-tab> </x-tab>my $alignio = new Bio::AlignIO('-format' =>
'fasta',</font></div>
<div><font
face="Courier New"><x-tab>
</x-tab><x-tab>
</x-tab><x-tab>
</x-tab><x-tab> </x-tab>
-interleaved => 0,</font></div>
<div><font
face="Courier New"><x-tab>
</x-tab><x-tab>
</x-tab><x-tab>
</x-tab><x-tab> </x-tab>
-file => $tempfile);<x-tab> </x-tab></font></div>
<div><font
face="Courier New"><x-tab>
</x-tab><x-tab>
</x-tab><x-tab>
</x-tab><x-tab>
</x-tab><x-tab> </x-tab><br>
<x-tab> </x-tab>my $aln =
$alignio->next_aln;<br>
<x-tab> </x-tab>my $codeml = new
Bio::Tools::Run::Phylo::PAML::Codeml();<br>
<x-tab>
</x-tab>#$codeml->no_param_checks(1);<x-tab>
</x-tab><br>
<x-tab>
</x-tab>$codeml->set_parameter('runmode',0);<br>
<x-tab>
</x-tab>$codeml->set_parameter('seqtype',1);<br>
<x-tab>
</x-tab>$codeml->set_parameter('CodonFreq',2);</font></div>
<div><font
face="Courier New"><x-tab>
</x-tab>$codeml->set_parameter('model', 1);</font></div>
<div><font
face="Courier New"><x-tab>
</x-tab>$codeml->set_parameter('NSsites', 0);</font></div>
<div><font
face="Courier New"><x-tab>
</x-tab>$codeml->set_parameter('fix_omega', 0);<br>
<x-tab> </x-tab>$codeml->set_parameter('omega',0.4);<br>
<x-tab>
</x-tab>$codeml->set_parameter('fix_kappa', 0);<br>
<x-tab> </x-tab>$codeml->set_parameter('kappa',2);<br>
<x-tab>
</x-tab>$codeml->set_parameter('cleandata',1);<br>
<x-tab> </x-tab><br>
<x-tab> </x-tab>print
$codeml->executable(), " is codeml\n";</font><br>
<font face="Courier New"></font></div>
<div><font
face="Courier New"><x-tab>
</x-tab>$codeml->alignment($aln); ## it gets to here and
tries to use $aln and gives the warning</font></div>
<div><font face="Courier New"><br></font></div>
<div><font face="Courier New">Thanks,</font></div>
<div><font face="Courier New"><br></font></div>
<div><font face="Courier New">Alisha</font></div>
<div><font face="Courier New"><br></font></div>
<div><br></div>
<x-sigsep><pre>--
</pre></x-sigsep>
<div>Alisha Holloway<br>
<br>
Postdoctoral Fellow<br>
Section of Evolution & Ecology<br>
3347 Storer Hall<br>
University of California<br>
Davis, CA 95616<br>
<br>
530-754-9551 Office<br>
512-297-3958 Cell<br>
530-752-1449 Fax</div>
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