[2015-02-20 18:07:40] Beginning TopHat run (v2.0.13)
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[2015-02-20 18:07:40] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2015-02-20 18:07:41] Checking for Bowtie index files (genome)..
[2015-02-20 18:07:41] Checking for reference FASTA file
[2015-02-20 18:07:41] Generating SAM header for /Volumes/web/halfshell/qdod3/Crassostrea_gigas.GCA_000297895.1.25.dna_sm.toplevel
[2015-02-20 18:07:54] Preparing reads
	 left reads: min. length=101, max. length=101, 18308054 kept reads (479804 discarded)
[2015-02-20 18:22:17] Mapping left_kept_reads to genome Crassostrea_gigas.GCA_000297895.1.25.dna_sm.toplevel with Bowtie2 
[2015-02-20 19:10:34] Mapping left_kept_reads_seg1 to genome Crassostrea_gigas.GCA_000297895.1.25.dna_sm.toplevel with Bowtie2 (1/4)
[2015-02-20 19:16:38] Mapping left_kept_reads_seg2 to genome Crassostrea_gigas.GCA_000297895.1.25.dna_sm.toplevel with Bowtie2 (2/4)
[2015-02-20 19:22:20] Mapping left_kept_reads_seg3 to genome Crassostrea_gigas.GCA_000297895.1.25.dna_sm.toplevel with Bowtie2 (3/4)
[2015-02-20 19:28:11] Mapping left_kept_reads_seg4 to genome Crassostrea_gigas.GCA_000297895.1.25.dna_sm.toplevel with Bowtie2 (4/4)
[2015-02-20 19:35:23] Searching for junctions via segment mapping
[2015-02-20 19:40:57] Retrieving sequences for splices
[2015-02-20 19:41:32] Indexing splices
[2015-02-20 19:42:46] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2015-02-20 19:45:27] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2015-02-20 19:48:10] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2015-02-20 19:50:49] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2015-02-20 19:53:28] Joining segment hits
[2015-02-20 19:59:41] Reporting output tracks
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[2015-02-20 20:13:34] A summary of the alignment counts can be found in 4M-HS/align_summary.txt
[2015-02-20 20:13:34] Run complete: 02:05:53 elapsed