question about GATK?

[loveseq]

Hi ,
this is the first time to use the software,
when I install it and run it using the example given on GATK wiki page,but the result is different .here is my result:
[renml@microcystis ~]$ java -jar GenomeAnalysisTK.jar -R exampleFASTA.fasta -I exampleBAM.bam -T CountLoci
INFO 14:03:05,468 HelpFormatter - ---------------------------------------------------------------------------
INFO 14:03:05,470 HelpFormatter - The Genome Analysis Toolkit (GATK) v1.0.4705, Compiled 2010/11/18 14:06:00
INFO 14:03:05,470 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 14:03:05,470 HelpFormatter - Please view our documentation at http://www.broadinstitute.org/gsa/wiki
INFO 14:03:05,471 HelpFormatter - For support, please view our support site at http://getsatisfaction.com/gsa
INFO 14:03:05,471 HelpFormatter - Program Args: -R exampleFASTA.fasta -I exampleBAM.bam -T CountLoci
INFO 14:03:05,471 HelpFormatter - Date/Time: 2010/11/24 14:03:05
INFO 14:03:05,471 HelpFormatter - ---------------------------------------------------------------------------
INFO 14:03:05,471 HelpFormatter - ---------------------------------------------------------------------------
INFO 14:03:05,472 AbstractGenomeAnalysisEngine - Strictness is SILENT
INFO 14:03:05,588 TraversalEngine - [INITIALIZATION COMPLETE; TRAVERSAL STARTING]
2026
INFO 14:03:05,718 TraversalEngine - [PROGRESS] Traversed 2,026 sites in 0.16 secs (79.47 secs per 1M sites)
INFO 14:03:05,719 TraversalEngine - Total runtime 0.16 secs, 0.00 min, 0.00 hours
INFO 14:03:05,720 TraversalEngine - 0 reads were filtered out during traversal out of 33 total (0.00%)
INFO 14:03:05,722 GATKRunReport - Aggregating data for run report




java version "1.6.0_21"
Java(TM) SE Runtime Environment (build 1.6.0_21-b06)
Java HotSpot(TM) 64-Bit Server VM (build 17.0-b16, mixed mode)


could anyone help me ?

[NGSfan]

I would recommend visiting their support forum:

http://getsatisfaction.com/gsa

they are very helpful and responsive.


Good luck!