[2014-05-29 20:27:45] Beginning TopHat run (v2.0.8b)
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[2014-05-29 20:27:45] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-29 20:27:45] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-29 20:27:46] Checking for Bowtie index files
[2014-05-29 20:27:46] Checking for reference FASTA file
[2014-05-29 20:27:46] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-29 20:27:48] Preparing reads
	 left reads: min. length=60, max. length=101, 21129319 kept reads (1125 discarded)
[2014-05-29 20:37:58] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-29 21:09:41] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-29 21:12:11] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-29 21:14:50] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-29 21:17:34] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-29 21:20:34] Searching for junctions via segment mapping
[2014-05-29 21:24:58] Retrieving sequences for splices
[2014-05-29 21:26:55] Indexing splices
[2014-05-29 21:27:31] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-29 21:28:43] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-29 21:30:06] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-29 21:31:30] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-29 21:32:47] Joining segment hits
[2014-05-29 21:36:16] Reporting output tracks
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[2014-05-29 21:49:23] Run complete: 01:21:37 elapsed