[2015-02-20 09:53:12] Beginning TopHat run (v2.0.13)
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[2015-02-20 09:53:12] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2015-02-20 09:53:13] Checking for Bowtie index files (genome)..
[2015-02-20 09:53:13] Checking for reference FASTA file
[2015-02-20 09:53:13] Generating SAM header for /Volumes/web/halfshell/qdod3/Crassostrea_gigas.GCA_000297895.1.25.dna_sm.toplevel
[2015-02-20 09:53:15] Preparing reads