[2014-04-25 18:35:02] Beginning TopHat run (v2.0.8b)
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[2014-04-25 18:35:02] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-25 18:35:02] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-25 18:35:02] Checking for Bowtie index files
[2014-04-25 18:35:02] Checking for reference FASTA file
[2014-04-25 18:35:02] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-25 18:35:05] Preparing reads
	 left reads: min. length=60, max. length=101, 24778284 kept reads (2604 discarded)
[2014-04-25 18:45:08] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-25 19:16:00] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-25 19:17:59] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-25 19:20:09] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-25 19:22:22] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-25 19:25:06] Searching for junctions via segment mapping
[2014-04-25 19:28:58] Retrieving sequences for splices
[2014-04-25 19:30:54] Indexing splices
[2014-04-25 19:31:37] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-25 19:32:31] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-25 19:33:35] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-25 19:34:39] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-25 19:35:44] Joining segment hits
[2014-04-25 19:39:00] Reporting output tracks
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[2014-04-25 19:53:23] Run complete: 01:18:20 elapsed