[2014-04-27 18:47:43] Beginning TopHat run (v2.0.8b)
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[2014-04-27 18:47:43] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-27 18:47:43] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-27 18:47:43] Checking for Bowtie index files
[2014-04-27 18:47:43] Checking for reference FASTA file
[2014-04-27 18:47:43] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-27 18:47:49] Preparing reads
	 left reads: min. length=60, max. length=101, 23959013 kept reads (14523 discarded)
[2014-04-27 18:57:15] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-27 19:27:51] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-27 19:31:37] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-27 19:35:37] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-27 19:39:34] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-27 19:43:55] Searching for junctions via segment mapping
[2014-04-27 20:52:09] Retrieving sequences for splices
[2014-04-27 20:54:05] Indexing splices
[2014-04-27 20:54:54] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-27 21:03:39] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-27 21:11:53] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-27 21:20:10] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-27 21:29:50] Joining segment hits
[2014-04-27 21:39:29] Reporting output tracks
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[2014-04-27 21:53:33] Run complete: 03:05:50 elapsed