[Bioperl-l] about PAML running within bioperl + bp_pairwise_kaks.pl

Caleb Davis cdavis at bcm.tmc.edu
Tue Sep 19 15:09:34 EDT 2006


Hi Zhuocheng,

This is the same error I was getting.  What version of PAML are you using? 

I refreshed bioperl-live and bioperl-run to the CVS version and then 
bp_pairwise_kaks reported that it doesn't work for 3.15.  The mlc file 
format must have changed and broke the parser.  I switched to PAML 3.14 
and then it worked great.

Thanks guys!
--Caleb

zhuocheng Hou wrote:
> Hello, every one,
>
> I use code in the PAML HOWTO (running PAML fom within Bioperl) on my Linux OS. And I set ENV as described by instructions. At the beginning, it seems that ClustalW run smoothly. However, when the programme run to call method "get_MLmatrix", somethign happened. The following information was listed as follows: (What reason or How to solve these problems?)
> ........
> Sequences (2:3) Aligned. Score:  87
> Sequences (2:4) Aligned. Score:  88
> Sequences (2:5) Aligned. Score:  87
> Sequences (2:6) Aligned. Score:  87
> Sequences (2:7) Aligned. Score:  87
> Sequences (2:8) Aligned. Score:  87
> Sequences (3:4) Aligned. Score:  93
> Sequences (3:5) Aligned. Score:  93
> Sequences (3:6) Aligned. Score:  93
> Sequences (3:7) Aligned. Score:  92
> Sequences (3:8) Aligned. Score:  92
> Sequences (4:5) Aligned. Score:  99
> Sequences (4:6) Aligned. Score:  99
> Sequences (4:7) Aligned. Score:  98
> Sequences (4:8) Aligned. Score:  98
> Sequences (5:6) Aligned. Score:  100
> Sequences (5:7) Aligned. Score:  99
> Sequences (5:8) Aligned. Score:  99
> Sequences (6:7) Aligned. Score:  99
> Sequences (6:8) Aligned. Score:  99
> Sequences (7:8) Aligned. Score:  100
> Guide tree        file created:   [/home/zchou/TMPDIR/8QEqLivAKY/JU833u8OTP.dnd]
> Start of Multiple Alignment
> There are 7 groups
> Aligning...
> Group 1: Sequences:   2      Score:5875
> Group 2: Sequences:   2      Score:5877
> Group 3: Sequences:   4      Score:5864
> Group 4: Sequences:   5      Score:5537
> Group 5: Sequences:   6      Score:5727
> Group 6: Sequences:   7      Score:5608
> Group 7: Sequences:   8      Score:5607
> Alignment Score 43650
> GCG-Alignment file created      [/home/zchou/TMPDIR/8QEqLivAKY/CussPD56rZ]
> aligned aa sequences were: Bio::SimpleAlign=HASH(0x87b93f4)
> Can't call method "get_MLmatrix" on an undefined value at originalpaml.pl line 57, <GEN2> line 332.
>
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> Zhuocheng Hou
> Department of Animal Genetics and Breeding
> China Agricultural University
>
>   
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>
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