[2014-04-26 16:35:36] Beginning TopHat run (v2.0.8b)
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[2014-04-26 16:35:36] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-26 16:35:36] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-26 16:35:36] Checking for Bowtie index files
[2014-04-26 16:35:36] Checking for reference FASTA file
[2014-04-26 16:35:36] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-26 16:35:38] Preparing reads
	 left reads: min. length=60, max. length=101, 24433033 kept reads (5059 discarded)
[2014-04-26 16:45:30] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-26 17:17:49] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-26 17:20:33] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-26 17:23:32] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-26 17:26:38] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-26 17:30:01] Searching for junctions via segment mapping
[2014-04-26 17:34:44] Retrieving sequences for splices
[2014-04-26 17:36:57] Indexing splices
[2014-04-26 17:37:34] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-26 17:39:06] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-26 17:40:56] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-26 17:42:46] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-26 17:44:24] Joining segment hits
[2014-04-26 17:48:40] Reporting output tracks
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[2014-04-26 18:06:22] Run complete: 01:30:46 elapsed