[Bioperl-l] about PAML running within bioperl

Georgii A Bazykin gbazykin at Princeton.EDU
Thu Oct 26 18:49:56 EDT 2006


I just had the exact same problem, which was also (as in Caleb Davis's
case) was solved by switching to PAML 3.14 from 3.15.


------------------------------
Tuesday, September 19, 2006, 5:40:07 AM, you 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.








> Zhuocheng Hou
> Department of Animal Genetics and Breeding
> China Agricultural University




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