Error in RNAseqc

Hi I am using the gtf file and reference fasta file linked on this page of RNAseqc (

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


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 :

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(
at org.broadinstitute.sting.utils.interval.IntervalUtils.intervalFileToList(
at org.broadinstitute.sting.utils.interval.IntervalUtils.parseIntervalArguments(
at org.broadinstitute.sting.commandline.IntervalBinding.getIntervals(
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.loadIntervals(
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.initializeIntervals(
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(
at org.broadinstitute.sting.commandline.CommandLineProgram.start(
at org.broadinstitute.sting.commandline.CommandLineProgram.start(
at org.broadinstitute.cga.rnaseq.gatk.GATKTools.runIntervalReadCounter(
at org.broadinstitute.cga.rnaseq.ReadCountMetrics.countrRNAIntervals(
at org.broadinstitute.cga.rnaseq.ReadCountMetrics.runReadCountMetrics(
at org.broadinstitute.cga.rnaseq.RNASeqMetrics.runMetrics(
at org.broadinstitute.cga.rnaseq.RNASeqMetrics.execute(
at org.broadinstitute.cga.rnaseq.RNASeqMetrics.main(

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.