[Bioperl-l] about PAML running within bioperl

[zhuocheng Hou]

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