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 firstname.lastname@example.org ============================================== 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.