It appears that your index files are not matching the reference files. That is likely the source of all the problems you have posted across several threads.
I would suggest getting the complete set of index, GTF and sequence files from one source so that they all match: http://cufflinks.cbcb.umd.edu/igenomes.html
I would suggest getting the complete set of index, GTF and sequence files from one source so that they all match: http://cufflinks.cbcb.umd.edu/igenomes.html
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