[2015-02-20 12:55:45] Beginning TopHat run (v2.0.13)
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[2015-02-20 12:55:45] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2015-02-20 12:55:46] Checking for Bowtie index files (genome)..
[2015-02-20 12:55:46] Checking for reference FASTA file
[2015-02-20 12:55:46] Generating SAM header for /Volumes/web/halfshell/qdod3/Crassostrea_gigas.GCA_000297895.1.25.dna_sm.toplevel
[2015-02-20 12:56:00] Preparing reads
	 left reads: min. length=101, max. length=101, 22797322 kept reads (17404 discarded)
[2015-02-20 13:13:43] Mapping left_kept_reads to genome Crassostrea_gigas.GCA_000297895.1.25.dna_sm.toplevel with Bowtie2 
[2015-02-20 13:59:12] Mapping left_kept_reads_seg1 to genome Crassostrea_gigas.GCA_000297895.1.25.dna_sm.toplevel with Bowtie2 (1/4)
[2015-02-20 14:04:57] Mapping left_kept_reads_seg2 to genome Crassostrea_gigas.GCA_000297895.1.25.dna_sm.toplevel with Bowtie2 (2/4)
[2015-02-20 14:10:52] Mapping left_kept_reads_seg3 to genome Crassostrea_gigas.GCA_000297895.1.25.dna_sm.toplevel with Bowtie2 (3/4)
[2015-02-20 14:16:55] Mapping left_kept_reads_seg4 to genome Crassostrea_gigas.GCA_000297895.1.25.dna_sm.toplevel with Bowtie2 (4/4)
[2015-02-20 14:24:32] Searching for junctions via segment mapping
[2015-02-20 14:31:27] Retrieving sequences for splices
[2015-02-20 14:32:05] Indexing splices
[2015-02-20 14:34:05] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2015-02-20 14:37:20] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2015-02-20 14:40:46] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2015-02-20 14:44:13] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2015-02-20 14:48:01] Joining segment hits
[2015-02-20 14:54:50] Reporting output tracks
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[2015-02-20 15:11:49] A summary of the alignment counts can be found in 2M-HS/align_summary.txt
[2015-02-20 15:11:49] Run complete: 02:16:03 elapsed