[2015-02-20 15:41:30] Beginning TopHat run (v2.0.13)
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[2015-02-20 15:41:30] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2015-02-20 15:41:30] Checking for Bowtie index files (genome)..
[2015-02-20 15:41:30] Checking for reference FASTA file
[2015-02-20 15:41:30] Generating SAM header for /Volumes/web/halfshell/qdod3/Crassostrea_gigas.GCA_000297895.1.25.dna_sm.toplevel
[2015-02-20 15:41:32] Preparing reads
	 left reads: min. length=101, max. length=101, 23807053 kept reads (88171 discarded)
[2015-02-20 16:00:09] Mapping left_kept_reads to genome Crassostrea_gigas.GCA_000297895.1.25.dna_sm.toplevel with Bowtie2 
[2015-02-20 16:50:34] Mapping left_kept_reads_seg1 to genome Crassostrea_gigas.GCA_000297895.1.25.dna_sm.toplevel with Bowtie2 (1/4)
[2015-02-20 16:56:59] Mapping left_kept_reads_seg2 to genome Crassostrea_gigas.GCA_000297895.1.25.dna_sm.toplevel with Bowtie2 (2/4)
[2015-02-20 17:03:24] Mapping left_kept_reads_seg3 to genome Crassostrea_gigas.GCA_000297895.1.25.dna_sm.toplevel with Bowtie2 (3/4)
[2015-02-20 17:09:56] Mapping left_kept_reads_seg4 to genome Crassostrea_gigas.GCA_000297895.1.25.dna_sm.toplevel with Bowtie2 (4/4)
[2015-02-20 17:18:11] Searching for junctions via segment mapping
[2015-02-20 17:25:13] Retrieving sequences for splices
[2015-02-20 17:25:52] Indexing splices
[2015-02-20 17:27:43] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2015-02-20 17:31:19] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2015-02-20 17:35:08] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2015-02-20 17:38:49] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2015-02-20 17:42:56] Joining segment hits
[2015-02-20 17:50:33] Reporting output tracks
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[2015-02-20 18:07:39] A summary of the alignment counts can be found in 4M/align_summary.txt
[2015-02-20 18:07:39] Run complete: 02:26:08 elapsed