[2014-12-18 15:34:15] Beginning TopHat run (v2.0.13)
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[2014-12-18 15:34:15] Checking for Bowtie
		  Bowtie version:	 2.2.3.0
[2014-12-18 15:34:15] Checking for Bowtie index files (genome)..
[2014-12-18 15:34:15] Checking for reference FASTA file
[2014-12-18 15:34:15] Generating SAM header for oyster.v9
[2014-12-18 15:34:28] Preparing reads
	 left reads: min. length=101, max. length=101, 22797322 kept reads (17404 discarded)
[2014-12-18 15:54:10] Mapping left_kept_reads to genome oyster.v9 with Bowtie2 
[2014-12-18 19:33:21] Mapping left_kept_reads_seg1 to genome oyster.v9 with Bowtie2 (1/4)
[2014-12-18 20:20:06] Mapping left_kept_reads_seg2 to genome oyster.v9 with Bowtie2 (2/4)
[2014-12-18 21:07:07] Mapping left_kept_reads_seg3 to genome oyster.v9 with Bowtie2 (3/4)
[2014-12-18 21:54:02] Mapping left_kept_reads_seg4 to genome oyster.v9 with Bowtie2 (4/4)
[2014-12-18 23:00:56] Searching for junctions via segment mapping