[Bioperl-l] trouble with pairwise_kaks.PLS on Cygwin/XP platform

Caleb Davis cdavis at bcm.tmc.edu
Mon Sep 18 18:15:06 EDT 2006


Hiyo,

I just switched from cygwin to solaris (perl 5.6.1, bioperl 1.5) and the 
pairwise_kaks.PLS script is falling a bit short for me there too.  I 
don't have the path issues anymore, but I am still getting the same 'Use 
of uninitialized value in pattern match (m//) at 
/users/cdavis/perlmodules/Bio/Tools/Phylo/PAML.pm line 711' error.  I 
checked Bio::Tools::Phylo::PAML.pm, and the offending line is 'return 
unless (/^Nei\s*\&\s*Gojobori/);'.  It's not within a loop, so maybe 
there's no $_ variable to match against?

I think most of the script is working fine.  If I check the temp 
directories I see all the files created by codeml, but the code fails 
when it tries to parse the mlc file.  Any help would be much appreciated.

Thanks,
--Caleb

Below are my command line, screen output, and mlc file:
------------command line, screen output-------------------
%perl pairwise_kaks.PLS -i worm_fam_2785.cdna



 CLUSTAL W (1.8) Multiple Sequence Alignments



Sequence format is Pearson
Sequence 1: CBG10100        363 aa
Sequence 2: F22B7.13        525 aa
Sequence 3: C38C10.4        525 aa
Start of Pairwise alignments
Aligning...
Sequences (1:2) Aligned. Score:  9
Sequences (1:3) Aligned. Score:  8
Sequences (2:3) Aligned. Score:  96
Guide tree        file created:   [/var/tmp/RPJTug0JLw/8t0wv2O5ht.dnd]
Start of Multiple Alignment
There are 2 groups
Aligning...
Group 1: Sequences:   2      Score:11215
Group 2:                     Delayed
Sequence:1     Score:2781
Alignment Score 3113
GCG-Alignment file created      [/var/tmp/RPJTug0JLw/xgCEKU3GhA]
Use of uninitialized value in pattern match (m//) at 
/users/cdavis/perlmodules/Bio/Tools/Phylo/PAML.pm line 711, <GEN2> line 105.
Can't call method "get_MLmatrix" on an undefined value at 
pairwise_kaks.PLS line 177, <GEN2> line 105.


---------------------mlc output file:----------------------------
CODONML (in paml 3.15, November 2005)    
/var/tmp/twy9U1wDNm/5Z2veeuziK   Model: One dN/dS ratio
Codon frequencies: F3x4
ns =   3  ls = 363

Codon usage in sequences
--------------------------------------------------------------------------
Phe TTT  4  4  7 | Ser TCT  3  4  4 | Tyr TAT  4  4  2 | Cys TGT  0  1  2
    TTC 14 14  7 |     TCC  2  4  4 |     TAC  8  7  5 |     TGC  3  2  1
Leu TTA  1  0  2 |     TCA  4  3  5 | *** TAA  0  0  0 | *** TGA  0  0  0
    TTG 10 10  6 |     TCG  9  9  5 |     TAG  0  0  0 | Trp TGG  1  1  2
--------------------------------------------------------------------------
Leu CTT  4  3  2 | Pro CCT  3  2  4 | His CAT  2  1  5 | Arg CGT  4  4  3
    CTC  6  7  5 |     CCC  2  1  5 |     CAC  2  4  2 |     CGC  1  1  2
    CTA  3  2  4 |     CCA  2  2  6 | Gln CAA  7  6 12 |     CGA  3  3 14
    CTG  7  8  6 |     CCG  2  2  3 |     CAG  6  7  4 |     CGG  1  1  3
--------------------------------------------------------------------------
Ile ATT  8 10 10 | Thr ACT  3  3  9 | Asn AAT 11 11 10 | Ser AGT  4  4  8
    ATC 12 12  2 |     ACC  4  4  4 |     AAC  8  7  5 |     AGC  5  6  4
    ATA  0  1  1 |     ACA  7  7 11 | Lys AAA 17 19 26 | Arg AGA  9  8 12
Met ATG 17 16 10 |     ACG  5  5  2 |     AAG 17 17  9 |     AGG  3  3  3
--------------------------------------------------------------------------
Val GTT  1  1  4 | Ala GCT  9  9  6 | Asp GAT 21 20 16 | Gly GGT  2  2  5
    GTC  4  4  4 |     GCC  8  7  6 |     GAC  5  5  4 |     GGC  2  2  4
    GTA  2  2  4 |     GCA  7  7  8 | Glu GAA 12 13 10 |     GGA 12 11  8
    GTG  9  9  8 |     GCG  3  3  3 |     GAG 17 17 14 |     GGG  1  1  1
--------------------------------------------------------------------------

Codon position x base (3x4) table for each sequence.

#1: F22B7.13      
position  1:    T:0.17355    C:0.15152    A:0.35813    G:0.31680
position  2:    T:0.28099    C:0.20110    A:0.37741    G:0.14050
position  3:    T:0.22865    C:0.23691    A:0.23691    G:0.29752

#2: C38C10.4      
position  1:    T:0.17355    C:0.14876    A:0.36639    G:0.31129
position  2:    T:0.28375    C:0.19835    A:0.38017    G:0.13774
position  3:    T:0.22865    C:0.23967    A:0.23140    G:0.30028

#3: CBG10100      
position  1:    T:0.14325    C:0.22039    A:0.34711    G:0.28926
position  2:    T:0.22590    C:0.23416    A:0.34160    G:0.19835
position  3:    T:0.26722    C:0.17631    A:0.33884    G:0.21763

Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT      15 | Ser S TCT      11 | Tyr Y TAT      10 | Cys C 
TGT       3
      TTC      35 |       TCC      10 |       TAC      20 |       
TGC       6
Leu L TTA       3 |       TCA      12 | *** * TAA       0 | *** * 
TGA       0
      TTG      26 |       TCG      23 |       TAG       0 | Trp W 
TGG       4
------------------------------------------------------------------------------
Leu L CTT       9 | Pro P CCT       9 | His H CAT       8 | Arg R 
CGT      11
      CTC      18 |       CCC       8 |       CAC       8 |       
CGC       4
      CTA       9 |       CCA      10 | Gln Q CAA      25 |       
CGA      20
      CTG      21 |       CCG       7 |       CAG      17 |       
CGG       5
------------------------------------------------------------------------------
Ile I ATT      28 | Thr T ACT      15 | Asn N AAT      32 | Ser S 
AGT      16
      ATC      26 |       ACC      12 |       AAC      20 |       
AGC      15
      ATA       2 |       ACA      25 | Lys K AAA      62 | Arg R 
AGA      29
Met M ATG      43 |       ACG      12 |       AAG      43 |       
AGG       9
------------------------------------------------------------------------------
Val V GTT       6 | Ala A GCT      24 | Asp D GAT      57 | Gly G 
GGT       9
      GTC      12 |       GCC      21 |       GAC      14 |       
GGC       8
      GTA       8 |       GCA      22 | Glu E GAA      35 |       
GGA      31
      GTG      26 |       GCG       9 |       GAG      48 |       
GGG       3
------------------------------------------------------------------------------


Codon position x base (3x4) table, overall

position  1:    T:0.16345    C:0.17355    A:0.35721    G:0.30579
position  2:    T:0.26354    C:0.21120    A:0.36639    G:0.15886
position  3:    T:0.24151    C:0.21763    A:0.26905    G:0.27181


Nei & Gojobori 1986. dN/dS (dN, dS)
(Note: This matrix is not used in later m.l. analysis.
Use runmode = -2 for ML pairwise comparison.)

F22B7.13           
C38C10.4             0.3605 (0.0142 0.0393)
CBG10100            -1.0000 (1.2263 -1.0000)-1.0000 (1.2584 -1.0000)

pairwise comparison, codon frequencies: F3x4.


2 (C38C10.4) ... 1 (F22B7.13)
lnL =-1564.430860
  0.05959  6.84008  0.57546

t= 0.0596  S=   329.1  N=   759.9  dN/dS= 0.5755  dN= 0.0162  dS= 0.0282

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