GATK::The contig index 20 is greater than the stored sequence count (1)

[Lessthan3]

Beginner in bioinformatics,

So when I use the GATK command

java -jar GenomeAnalysisTK.jar -I MYBAM.bam -R MYFASTA.fa -T CountReads

I get the following error:

INFO  15:46:15,479 HelpFormatter - --------------------------------------------------------------------------------- 
INFO  15:46:15,481 HelpFormatter - The Genome Analysis Toolkit (GATK) v1.6-13-g91f02df, Compiled 2012/06/26 20:27:56 .orgftp://[email protected]
INFO  15:46:15,481 HelpFormatter - Copyright (c) 2010 The Broad Institute bam -R chr21.fa -T CountReads
INFO  15:46:15,481 HelpFormatter - Please view our documentation at http://www.broadinstitute.org/gsa/wiki 
INFO  15:46:15,481 HelpFormatter - For support, please view our support site at http://getsatisfaction.com/gsa 
INFO  15:46:15,482 HelpFormatter - Program Args: -I sorted_indexed.bam -R chr21.fa -T CountReads 
INFO  15:46:15,482 HelpFormatter - Date/Time: 2012/07/23 15:46:15 
INFO  15:46:15,483 HelpFormatter - --------------------------------------------------------------------------------- 
INFO  15:46:15,483 HelpFormatter - --------------------------------------------------------------------------------- 
INFO  15:46:15,487 GenomeAnalysisEngine - Strictness is SILENT 
INFO  15:46:15,526 SAMDataSource$SAMReaders - Initializing SAMRecords in serial 
INFO  15:46:15,546 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02 
INFO  15:46:16,278 GATKRunReport - Uploaded run statistics report to AWS S3 
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 1.6-13-g91f02df): 
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki
##### ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa
##### ERROR
##### ERROR MESSAGE: Badly formed genome loc: Parameters to GenomeLocParser are incorrect:The contig index 20 is greater than the stored sequence count (1)
##### ERROR ------------------------------------------------------------------------------------------

I sorted MYBAM, added read groups, and indexed it.
The MYBAM corresponds to chromosome 21, and I got MYFASTA from http://hgdownload.cse.ucsc.edu/golde...8/chromosomes/ for chr21.

Please help solve this.

Thanks!