[Bioperl-l] trouble with pairwise_kaks.PLS on Cygwin/XP platform
Caleb Davis
cdavis at bcm.tmc.edu
Mon Sep 18 22:15:06 UTC 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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Subject: Re: [Bioperl-l] trouble with pairwise_kaks.PLS on Cygwin/XP platform
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