[Biojava-l] error: Program ncbi-blastn Version 2.2.17 is not supported

[Allan Kamau]

Hi all,
I've searched for a conclusive answer to the "Program ncbi-blastn 
Version <some value> is not supported" without success.
I would like to know format of the blast output the Biojava's blast-like 
parsing framework likes, including some examples (without the data) of 
how such blast output may be created.
For example, I am using ncbi-blastn and I am generating the blast file 
(which Biojava doesn't like) as follows.

export FORMATDB=/usr/local/share/blast/blast-2.2.17/bin/formatdb;
export BLASTALL=/usr/local/share/blast/blast-2.2.17/bin/blastall;
export REFERENCES_FASTA_NAME=/study/tmp/somesequence/blast/20071017.fasta;
export BLAST_REPORT_TABULAR=somesequence.blast.txt
export BLAST_REPORT_XML=somesequence.blast.xml
export BLAST_REPORT=somesequence.blast
export INPUT_FASTA=somesequence.fasta
export WORK_DIR=/development/study/try1/tmpDataFiles/somesequence

date;time cd $WORK_DIR;cp $REFERENCES_FASTA_NAME .;$FORMATDB -i 
$REFERENCES_FASTA_NAME -p F -o T;echo `pwd`;$BLASTALL -p blastn -d 
$REFERENCES_FASTA_NAME -i $INPUT_FASTA -q -1 -r 1 -m 8 -o 
$BLAST_REPORT_TABULAR;$BLASTALL -p blastn -d $REFERENCES_FASTA_NAME -i 
$INPUT_FASTA -q -1 -r 1 -m 7 -o $BLAST_REPORT_XML;date;

Then I supply the $BLAST_REPORT as an argument to "BlastParser" copied 
from "http://biojava.org/wiki/BioJava:CookBook:Blast:Parser"

Then I get the error below.


[aaron at localhost try1]$ $ANT_HOME/bin/ant runBlastParser;
Buildfile: build.xml

runBlastParser:
     [java] org.xml.sax.SAXException: Program ncbi-blastn Version 2.2.17 
is not supported by the biojava blast-like parsing framework
     [java]     at 
org.biojava.bio.program.sax.BlastLikeSAXParser.interpret(BlastLikeSAXParser.java:241)
     [java]     at 
org.biojava.bio.program.sax.BlastLikeSAXParser.parse(BlastLikeSAXParser.java:160)

Allan.