[2015-02-23 15:38:55] Beginning TopHat run (v2.0.13)
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[2015-02-23 15:38:55] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2015-02-23 15:38:56] Checking for Bowtie index files (genome)..
[2015-02-23 15:38:56] Checking for reference FASTA file
[2015-02-23 15:38:56] Generating SAM header for /Volumes/web/halfshell/qdod3/Crassostrea_gigas.GCA_000297895.1.25.dna_sm.toplevel
[2015-02-23 15:39:08] Preparing reads
	 left reads: min. length=101, max. length=101, 28690571 kept reads (163825 discarded)
[2015-02-23 15:59:45] Mapping left_kept_reads to genome Crassostrea_gigas.GCA_000297895.1.25.dna_sm.toplevel with Bowtie2 
[2015-02-23 16:53:43] Mapping left_kept_reads_seg1 to genome Crassostrea_gigas.GCA_000297895.1.25.dna_sm.toplevel with Bowtie2 (1/4)
[2015-02-23 17:00:06] Mapping left_kept_reads_seg2 to genome Crassostrea_gigas.GCA_000297895.1.25.dna_sm.toplevel with Bowtie2 (2/4)
[2015-02-23 17:06:25] Mapping left_kept_reads_seg3 to genome Crassostrea_gigas.GCA_000297895.1.25.dna_sm.toplevel with Bowtie2 (3/4)
[2015-02-23 17:12:42] Mapping left_kept_reads_seg4 to genome Crassostrea_gigas.GCA_000297895.1.25.dna_sm.toplevel with Bowtie2 (4/4)
[2015-02-23 17:21:18] Searching for junctions via segment mapping
[2015-02-23 17:28:26] Retrieving sequences for splices
[2015-02-23 17:29:03] Indexing splices
[2015-02-23 17:31:03] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2015-02-23 17:34:16] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2015-02-23 17:37:38] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2015-02-23 17:40:58] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2015-02-23 17:44:49] Joining segment hits
[2015-02-23 17:52:18] Reporting output tracks
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[2015-02-23 18:11:36] A summary of the alignment counts can be found in ./tophat_out/align_summary.txt
[2015-02-23 18:11:36] Run complete: 02:32:40 elapsed