[2014-04-27 16:14:14] Beginning TopHat run (v2.0.8b)
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[2014-04-27 16:14:14] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-27 16:14:14] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-27 16:14:14] Checking for Bowtie index files
[2014-04-27 16:14:14] Checking for reference FASTA file
[2014-04-27 16:14:14] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-27 16:14:21] Preparing reads
	 left reads: min. length=60, max. length=101, 20813113 kept reads (14167 discarded)
[2014-04-27 16:22:29] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-27 16:48:34] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-27 16:52:05] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-27 16:55:39] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-27 16:59:11] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-27 17:02:57] Searching for junctions via segment mapping
[2014-04-27 17:53:47] Retrieving sequences for splices
[2014-04-27 17:55:44] Indexing splices
[2014-04-27 17:56:30] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-27 18:04:32] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-27 18:11:45] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-27 18:18:40] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-27 18:27:07] Joining segment hits
[2014-04-27 18:35:43] Reporting output tracks
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[2014-04-27 18:47:42] Run complete: 02:33:27 elapsed