[Bioperl-guts-l] [Bug 2782] New: Bio::Tools::Run::Phylo::Phylip::SeqBoot WON'T RUN

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Thu Mar 5 12:00:57 EST 2009


http://bugzilla.open-bio.org/show_bug.cgi?id=2782

           Summary: Bio::Tools::Run::Phylo::Phylip::SeqBoot WON'T RUN
           Product: BioPerl
           Version: unspecified
          Platform: Sun
        OS/Version: SunOS
            Status: NEW
          Severity: normal
          Priority: P2
         Component: bioperl-run
        AssignedTo: bioperl-guts-l at bioperl.org
        ReportedBy: j.m.herbert at bham.ac.uk


Hi there.
I can't get seqboot to work (from phylip) with the
Bio::Tools::Run::Phylo::Phylip::SeqBoot package. I use the example script, only
changing the protein file it needs and it can't find the infile needed by
seqboot. Please can you help me fix this problem? Thanks a lot. 

John.
# PROGRAM MADE AND RAN ==================================

#!/usr/bin/perl
use Bio::Tools::Run::Phylo::Phylip::SeqBoot;
use Bio::Tools::Run::Alignment::Clustalw;   
#Create a SimpleAlign object

  @params = ('ktuple' => 2, 'matrix' => 'BLOSUM');
  $factory = Bio::Tools::Run::Alignment::Clustalw->new(@params);
  $inputfilename = './prots';
  $aln = $factory->align($inputfilename); # $aln is a SimpleAlign object.

  # Use seqboot to generate bootstap alignments
  my @params = ('datatype'=>'SEQUENCE','replicates'=>100);
  my $seq = Bio::Tools::Run::Phylo::Phylip::SeqBoot->new(@params);

  my $aln_ref = $seq->run($aln);

  my $aio = Bio::AlignIO->new(-file=>">alignment.bootstrap",-format=>"phylip");
  foreach my $ai(@{$aln_ref}){
         $aio->write_aln($ai);
  }
#================== OUTPUT FROM THIS PROGRAM =====================

jherbert at orac [rhbdf2_xenopus]$ ./test.pl 



 CLUSTAL W (1.83) Multiple Sequence Alignments



Sequence format is Pearson
Sequence 1: h_rhbdf1        855 aa
Sequence 2: x_rhbdf1        292 aa
Start of Pairwise alignments
Aligning...
Sequences (1:2) Aligned. Score:  77
Guide tree        file created:   [./prots.dnd]
Start of Multiple Alignment
There are 1 groups
Aligning...
Group 1: Sequences:   2      Score:4867
Alignment Score 1553
GCG-Alignment file created      [/tmp/xsUHP13FGA/PgxpwKJ9Yz]
seqboot: can't find input file "infile"
Please enter a new file name> 

Bootstrapping algorithm, version 3.63

Settings for this run:
  D      Sequence, Morph, Rest., Gene Freqs?  Molecular sequences
  J  Bootstrap, Jackknife, Permute, Rewrite?  Bootstrap
  %    Regular or altered sampling fraction?  regular
  B      Block size for block-bootstrapping?  1 (regular bootstrap)
  R                     How many replicates?  100
  W              Read weights of characters?  No
  C                Read categories of sites?  No
  S     Write out data sets or just weights?  Data sets
  I             Input sequences interleaved?  Yes
  0      Terminal type (IBM PC, ANSI, none)?  ANSI
  1       Print out the data at start of run  No
  2     Print indications of progress of run  Yes

  Y to accept these or type the letter for one to change
Not a possible option!

Bootstrapping algorithm, version 3.63

Settings for this run:
  D      Sequence, Morph, Rest., Gene Freqs?  Molecular sequences
  J  Bootstrap, Jackknife, Permute, Rewrite?  Bootstrap
  %    Regular or altered sampling fraction?  regular
  B      Block size for block-bootstrapping?  1 (regular bootstrap)
  R                     How many replicates?  100
  W              Read weights of characters?  No
  C                Read categories of sites?  No
  S     Write out data sets or just weights?  Data sets
  I             Input sequences interleaved?  Yes
  0      Terminal type (IBM PC, ANSI, none)?  ANSI
  1       Print out the data at start of run  No
  2     Print indications of progress of run  Yes

  Y to accept these or type the letter for one to change
Number of replicates?

Bootstrapping algorithm, version 3.63

Settings for this run:
  D      Sequence, Morph, Rest., Gene Freqs?  Molecular sequences
  J  Bootstrap, Jackknife, Permute, Rewrite?  Bootstrap
  %    Regular or altered sampling fraction?  regular
  B      Block size for block-bootstrapping?  1 (regular bootstrap)
  R                     How many replicates?  100
  W              Read weights of characters?  No
  C                Read categories of sites?  No
  S     Write out data sets or just weights?  Data sets
  I             Input sequences interleaved?  Yes
  0      Terminal type (IBM PC, ANSI, none)?  ANSI
  1       Print out the data at start of run  No
  2     Print indications of progress of run  Yes

  Y to accept these or type the letter for one to change
Random number seed (must be odd)?
Random number seed (must be odd)?
Random number seed (must be odd)?
Random number seed (must be odd)?
Random number seed (must be odd)?
Random number seed (must be odd)?
Random number seed (must be odd)?
Random number seed (must be odd)?
Random number seed (must be odd)?
Random number seed (must be odd)?

ERROR: Made 10 attempts to read input in loop. Aborting run.

------------- EXCEPTION  -------------
MSG: SeqBoot did not create files correctly (/tmp/3EVNzzxryA/outfile)
STACK Bio::Tools::Run::Phylo::Phylip::SeqBoot::_run
/usr/local/lib/perl5/site_perl/5.8.3/Bio/Tools/Run/Phylo/Phylip/SeqBoot.pm:361
STACK Bio::Tools::Run::Phylo::Phylip::SeqBoot::run
/usr/local/lib/perl5/site_perl/5.8.3/Bio/Tools/Run/Phylo/Phylip/SeqBoot.pm:311
STACK toplevel ./test.pl:17

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