[2014-05-27 12:04:27] Beginning TopHat run (v2.0.8b)
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[2014-05-27 12:04:27] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-27 12:04:27] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-27 12:04:27] Checking for Bowtie index files
[2014-05-27 12:04:27] Checking for reference FASTA file
[2014-05-27 12:04:27] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-27 12:04:29] Preparing reads
	 left reads: min. length=60, max. length=101, 30354474 kept reads (566 discarded)
[2014-05-27 12:16:45] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-27 13:02:29] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-27 13:06:01] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-27 13:09:45] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-27 13:13:33] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-27 13:16:47] Searching for junctions via segment mapping
[2014-05-27 13:20:55] Retrieving sequences for splices
[2014-05-27 13:22:57] Indexing splices
[2014-05-27 13:23:45] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-27 13:26:11] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-27 13:28:54] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-27 13:31:31] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-27 13:33:58] Joining segment hits
[2014-05-27 13:37:39] Reporting output tracks
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[2014-05-27 13:53:12] Run complete: 01:48:44 elapsed