[2015-02-20 10:01:41] Beginning TopHat run (v2.0.13)
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[2015-02-20 10:01:41] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2015-02-20 10:01:41] Checking for Bowtie index files (genome)..
[2015-02-20 10:01:41] Checking for reference FASTA file
[2015-02-20 10:01:41] Generating SAM header for /Volumes/web/halfshell/qdod3/Crassostrea_gigas.GCA_000297895.1.25.dna_sm.toplevel
[2015-02-20 10:01:44] Preparing reads
	 left reads: min. length=101, max. length=101, 28690571 kept reads (163825 discarded)
[2015-02-20 10:24:29] Mapping left_kept_reads to genome Crassostrea_gigas.GCA_000297895.1.25.dna_sm.toplevel with Bowtie2 
[2015-02-20 11:26:21] Mapping left_kept_reads_seg1 to genome Crassostrea_gigas.GCA_000297895.1.25.dna_sm.toplevel with Bowtie2 (1/4)
[2015-02-20 11:34:07] Mapping left_kept_reads_seg2 to genome Crassostrea_gigas.GCA_000297895.1.25.dna_sm.toplevel with Bowtie2 (2/4)
[2015-02-20 11:41:45] Mapping left_kept_reads_seg3 to genome Crassostrea_gigas.GCA_000297895.1.25.dna_sm.toplevel with Bowtie2 (3/4)
[2015-02-20 11:49:29] Mapping left_kept_reads_seg4 to genome Crassostrea_gigas.GCA_000297895.1.25.dna_sm.toplevel with Bowtie2 (4/4)
[2015-02-20 11:59:19] Searching for junctions via segment mapping
[2015-02-20 12:07:49] Retrieving sequences for splices
[2015-02-20 12:08:27] Indexing splices
[2015-02-20 12:10:31] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2015-02-20 12:14:15] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2015-02-20 12:18:15] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2015-02-20 12:22:11] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2015-02-20 12:26:35] Joining segment hits
[2015-02-20 12:35:27] Reporting output tracks
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[2015-02-20 12:55:44] A summary of the alignment counts can be found in 2M/align_summary.txt
[2015-02-20 12:55:44] Run complete: 02:54:03 elapsed