[2015-02-21 10:03:19] Beginning TopHat run (v2.0.13)
-----------------------------------------------
[2015-02-21 10:03:19] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2015-02-21 10:03:19] Checking for Bowtie index files (genome)..
[2015-02-21 10:03:19] Checking for reference FASTA file
[2015-02-21 10:03:19] Generating SAM header for /Volumes/web/halfshell/qdod3/Crassostrea_gigas.GCA_000297895.1.25.dna_sm.toplevel
[2015-02-21 10:03:25] Preparing reads
	 left reads: min. length=101, max. length=101, 18099982 kept reads (864606 discarded)
[2015-02-21 10:17:35] Mapping left_kept_reads to genome Crassostrea_gigas.GCA_000297895.1.25.dna_sm.toplevel with Bowtie2 
[2015-02-21 11:05:39] Mapping left_kept_reads_seg1 to genome Crassostrea_gigas.GCA_000297895.1.25.dna_sm.toplevel with Bowtie2 (1/4)
[2015-02-21 11:11:59] Mapping left_kept_reads_seg2 to genome Crassostrea_gigas.GCA_000297895.1.25.dna_sm.toplevel with Bowtie2 (2/4)
[2015-02-21 11:17:33] Mapping left_kept_reads_seg3 to genome Crassostrea_gigas.GCA_000297895.1.25.dna_sm.toplevel with Bowtie2 (3/4)
[2015-02-21 11:23:07] Mapping left_kept_reads_seg4 to genome Crassostrea_gigas.GCA_000297895.1.25.dna_sm.toplevel with Bowtie2 (4/4)
[2015-02-21 11:29:26] Searching for junctions via segment mapping
[2015-02-21 11:33:14] Retrieving sequences for splices
[2015-02-21 11:33:48] Indexing splices
[2015-02-21 11:34:41] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2015-02-21 11:36:27] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2015-02-21 11:38:16] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2015-02-21 11:40:04] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2015-02-21 11:41:59] Joining segment hits
[2015-02-21 11:46:04] Reporting output tracks
-----------------------------------------------
[2015-02-21 11:57:24] A summary of the alignment counts can be found in 6M-HS/align_summary.txt
[2015-02-21 11:57:24] Run complete: 01:54:05 elapsed