I did not pay close attention to your original question (i.e. you are getting the error while running tophat itself and not the actual script). My fault.
Let us start over.
Is caref_ncbiall available in the same directory that you are running tophat from? If not, can you provide the full path to that file when you execute tophat. The same should apply to cp04.fastq and caref_seq.gff. Also make certain that your gff file matches the format specification as noted here: http://cufflinks.cbcb.umd.edu/gff.html
Let us start over.
Is caref_ncbiall available in the same directory that you are running tophat from? If not, can you provide the full path to that file when you execute tophat. The same should apply to cp04.fastq and caref_seq.gff. Also make certain that your gff file matches the format specification as noted here: http://cufflinks.cbcb.umd.edu/gff.html
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