[Bioperl-l] Troubleshooting blastcl3/BlastReport

[Karalius, Joseph]

Hello All,

I'm having trouble getting BlastReport to correctly parse my blast results
obtained from NCBI/Genbank using blastcl3.  BlastReport identifies the
correct number of sequences in the batch query, but does not recognize that
the queried sequences do in fact have significant alignments.  I'm using
Windows 2000 with ActivePerl.

Here is the BlastReport output:

C:\blast>perl c:\blast\blastreport\br2.pl

==== Begin BlastReport Parameter Selection ====


>Enter chromosome number of blast report to use or Q to quit.
0

blout_00 files:

 1 blout_00.txt
 2 blout_00_gisall.txt
 3 blout_00.gisall.20021104.txt

>Enter number of file to use or Q to quit: 3

Using file: blout_00.gisall.20021104.txt

Select type of Input:

  1  Marker
  2  cDNA

>Enter number for type of file or Q to quit: 1

Type of file selected: Marker


====     Begin BlastReport Execution       ====

INFO: BLASTIN opened successfully:
      c:\blast\out\blout_00.gisall.20021104.txt
INFO: Number of Query Sequences in the run:           247
INFO: Number of Query Sequences with alignments:      0
INFO: Sequences that may have significant alignments: 0
INFO: Full Report: c:\blast\out\BRept_00.gisall.20021104.txt_Full
INFO: Summary:     c:\blast\out\BRept_00.gisall.20021104.txt_Sum
INFO: Excel Table: c:\blast\out\BRept_00.gisall.20021104.txt_Tab


====   BlastReport Execution Completed     ====


C:\blast>


Has anyone else run into this problem before?  I'm using the latest version
of the BR script and can't seem to find any parameters that could be
modified to fix this problem.  As I understand the program it does not does
not define the significance of alignments it only summarizes the information
produced from blastcl3.  I can post the BR script I'm using and a BLAST
reults page if necessary.

Your help is appreciated,

Joey Karalius