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

Caleb F. Davis cdavis at bcm.tmc.edu
Fri Sep 1 00:00:59 UTC 2006

Hi folks,

Thank you for all your hard work with Bioperl.  My name is Caleb Davis, 
a first year grad student at Baylor College of Medicine.  I'm trying to 
use bioperl on a WinXP/cygwin configuration.  I've got it working great 
for everything up to this point.  I can read and write files, use the 
wrappers around bl2seq, etc.  However, I am now getting starting using 
PAML, and I am stuck.  I could not find anyone with my problem on the 
mailing list so I thought I'd ask you.

I'm using pairwise_kaks.PLS code and sample data to test my machine 
configuration first.  The code fails in various ways, and I can't figure 
out why.  I'm guessing it has something to do with the tmpdir 
environmental variable and the differences between windows and unix 
paths, but that's a stab in the dark really.

Will you point me in the right direction?  Thanks,

Included below are:

output of the command:
pairwise_kaks.PLS -i ~/src/bioperl/bioperl-live/t/data/worm_fam_2785.cdna
my environmental variables set in .bashrc


CLUSTAL W (1.83) 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
Sequences (1:2) Aligned. Score:  9
Sequences (1:3) Aligned. Score:  8
Sequences (2:3) Aligned. Score:  96
Guide tree        file created:   
Start of Multiple Alignment
There are 2 groups
Group 1: Sequences:   2      Score:11215
Group 2:                     Delayed
Sequence:1     Score:2745
Alignment Score 3187
GCG-Alignment file created      
Can't remove directory C:/cygwin/home/cdavis/tmp/Yqsvs4wNAX: Directory 
not empty at /usr/lib/perl5/site_perl/5.8/Bio/Root/IO.pm line 811
Use of uninitialized value in pattern match (m//) at 
/usr/lib/perl5/site_perl/5.8/Bio/Tools/Phylo/PAML.pm line 615, <GEN2> 
line 105.
Can't call method "get_MLmatrix" on an undefined value at 
./pairwise_kaks.PLS line 177, <GEN2> line 105.
#BioPerl settings
export BIOPERL_INDEX=~/bioperlindex
export TMPDIR=C:/cygwin/home/cdavis/tmp/

#Blast settings
export PATH=~/src/ncbi/blast-2.2.14/bin:${PATH}
export BLASTDIR=~/src/ncbi/blast-2.2.14
export BLASTDB=~/src/ncbi/blast-2.2.14/data

#other program settings
export CLUSTALDIR=~/bioperl-runnables/clustalw1.83
export PAMLDIR=~/bioperl-runnables/paml3.15/bin

#FTP settings
export FTP_PASV=1

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