Error in RNAseqc

Hi I am using the gtf file and reference fasta file linked on this page of RNAseqc (http://www.broadinstitute.org/cancer/cga/rnaseqc_download)

I have used the following step before running RNAseqc :-

1.) Create bowtie index using the reference fasta : Homo_sapiens_assembly19.fasta

renamed to Homo_sapiens.fa before running bowtie2-build

(http://www.broadinstitute.org/cancer/cga/sites/default/files/data/tools/...)

2.) Run tophat on the RNA-seq reads using the generated bowtie index

3.) Use picard tools AddOrReplaceReadGroups,ReorderSam and SortSam commands to make the bam files acceptable by RNA-seqc

4.) Run RNA-seqc using the following command :-

java -jar RNA-SeQC_v1.1.7.jar -n 1000 -s "GSM438363|GSM438363_sorted.bam|GSM438363" -t Homo_sapiens.GRCh37.72.gtf -r /home/skhan/data/Reference_files/Homo_sapiens_assembly19_bowtie2_index/Homo_sapiens.fa -o ./testReport/ -strat gc -gc gencode.v7.gc.txt

the gencode.v7.gc.txt file was downloaded from : http://www.broadinstitute.org/cancer/cga/sites/default/files/data/tools/...

This is the error I am getting :

org.broadinstitute.sting.utils.exceptions.UserException$MalformedGenomeLoc: Badly formed genome loc: Contig 'HG905_PATCH' does not match any contig in the GATK sequence dictionary derived from the reference; are you sure you are using the correct reference fasta file?
at org.broadinstitute.sting.utils.GenomeLocParser.parseGenomeLoc(GenomeLocParser.java:383)
at org.broadinstitute.sting.utils.interval.IntervalUtils.intervalFileToList(IntervalUtils.java:139)
at org.broadinstitute.sting.utils.interval.IntervalUtils.parseIntervalArguments(IntervalUtils.java:71)
at org.broadinstitute.sting.commandline.IntervalBinding.getIntervals(IntervalBinding.java:106)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.loadIntervals(GenomeAnalysisEngine.java:616)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.initializeIntervals(GenomeAnalysisEngine.java:583)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:233)
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:236)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:146)
at org.broadinstitute.cga.rnaseq.gatk.GATKTools.runIntervalReadCounter(GATKTools.java:152)
at org.broadinstitute.cga.rnaseq.ReadCountMetrics.countrRNAIntervals(ReadCountMetrics.java:231)
at org.broadinstitute.cga.rnaseq.ReadCountMetrics.runReadCountMetrics(ReadCountMetrics.java:63)
at org.broadinstitute.cga.rnaseq.RNASeqMetrics.runMetrics(RNASeqMetrics.java:220)
at org.broadinstitute.cga.rnaseq.RNASeqMetrics.execute(RNASeqMetrics.java:166)
at org.broadinstitute.cga.rnaseq.RNASeqMetrics.main(RNASeqMetrics.java:135)

I cannot figure out how can I get around this error. Kindly suggest what to do.

different contigs in gtf and ref fasta file

You probably have different contigs/chromosomes in the Homosapiens.fa and Homo_sapiens.GRCh37.72.gtf. Contigs in gtf file should be a complete subset of contigs in fasta file. You need to remove all the lines from gtf with contigs which don't match with the fasta file.