I am trying to use Lazarus, which is an ancestral reconstruction program using PAML, on a set of protein sequences.
The Lazarus portion of things seems to be working just fine, I invoked with pretty much standard parameters:

==============================================
  LAZARUS for PAML version June.28.2012
  questions? contact Victor Hanson-Smith
                  at victorhs@cs.uoregon.edu
==============================================

Settings for this run:

  D    datatype                 => amino acid
  A    sequence alignment file  => fp.fasta
            => O.K. I found 305 taxa.
  T    newick tree file         => fp.newick
            => O.K. I found 1 tree(s).
  P    path to folder w/ models => /home/nimaemami/Lazarus/Lazarus/paml/dat
            => O.K. I found 17 models named with *.dat or *.rates
  M    evolutionary model       => JTT
  B    branch lengths           => find ML estimate
  V    rate of evolution        => use 4 gamma-distributed categories
  O    output to this location  => /home/nimaemami/FPs
  I    place ancestral gaps     => No, I'll manually do it later.
  U    outgroup taxa            => ['259','167']




Are these settings correct? (type Y or letter to change option)Y
Invoking Lazarus with this command:
lazarus_batch --codeml --outputdir /home/nimaemami/FPs --alignment fp.fasta --tree fp.newick --model /home/nimaemami/Lazarus/Lazarus/paml/dat/jones.dat --branch_lengths estimate --asrv 4 --outgroup [['259','167']]
2.7.1+ (r271:86832, Apr 11 2011, 18:13:53)
[GCC 4.5.2]
--> Importing your files. . .
I found your alignment file: fp.fasta
...it appears to contain 305 taxon.
I found your tree file: fp.newick
...it appears to contain 1 trees.
/home/nimaemami/Lazarus/Lazarus/paml/dat/jones.dat
/home/nimaemami/Lazarus/Lazarus/paml/dat/jones.dat
I found your evolutionary model at: /home/nimaemami/Lazarus/Lazarus/paml/dat/jones.dat
/home/nimaemami/FPs
--> Starting PAML jobs. . .

Once it starts calling PAML, though, it is encountering the following error:

Error: initial value alpha <= 0 for fix_alpha = 0.
Hmmm, The PAML job on tree 1 did not produce a file named 'out.paml'.  I was expecting to find this file at /home/nimaemami/FPs/tree1/pamlWorkspace/out.paml

Has anybody encountered this before? I don't think the problem is the Lazarus model I'm using, since I tried another model and got the same result. It seems like there is some internal PAML parameter that I didn't touch that is breaking things. Any insight into how to get around this would be greatly appreciated.

-Nima