[2014-04-25 21:25:26] Beginning TopHat run (v2.0.8b)
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[2014-04-25 21:25:26] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-25 21:25:26] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-25 21:25:26] Checking for Bowtie index files
[2014-04-25 21:25:26] Checking for reference FASTA file
[2014-04-25 21:25:26] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-25 21:25:30] Preparing reads
	 left reads: min. length=60, max. length=101, 28220696 kept reads (8298 discarded)
[2014-04-25 21:36:49] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-25 22:12:53] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-25 22:15:46] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-25 22:19:00] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-25 22:23:05] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-25 22:26:35] Searching for junctions via segment mapping
[2014-04-25 22:31:00] Retrieving sequences for splices
[2014-04-25 22:32:56] Indexing splices
[2014-04-25 22:33:41] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-25 22:34:49] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-25 22:36:11] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-25 22:37:33] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-25 22:38:52] Joining segment hits
[2014-04-25 22:42:38] Reporting output tracks
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[2014-04-25 22:58:26] Run complete: 01:32:59 elapsed