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====Run RNA-SeQC v1.1.7.jar==== java -jar /home/kunzhang/softwares/RNA-SeQC_v1.1.7.jar -bwa /home/kunzhang/softwares/bwa-0.7.5a/ -BWArRNA ~/Genomes/RNA-SeqCResources/human_all_rRNA.fasta -s ~/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_samples.txt -t ~/Genomes/RNA-SeqCResources/gencode.v7.annotation.gtf -r ~/Genomes/HsGenome19.fa -o ~/scratch/RanHex_EnrichmRNA/inVitroRTSeq/RNA-SeQC_output/ -strat gc -gc ~/Genomes/RNA-SeqCResources/gencode.v7.gc.txt -singleEnd org.broadinstitute.sting.utils.exceptions.UserException$LexicographicallySortedSequenceDictionary: Lexicographically sorted human genome sequence detected in reads. For safety's sake the GATK requires human contigs in karyotypic order: 1, 2, ..., 10, 11, ..., 20, 21, 22, X, Y with M either leading or trailing these contigs. This is because all distributed GATK resources are sorted in karyotypic order, and your processing will fail when you need to use these files. You can use the ReorderSam utility to fix this problem: http://www.broadinstitute.org/gsa/wiki/index.php/ReorderSam
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