[2014-04-28 15:53:23] Beginning TopHat run (v2.0.8b)
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[2014-04-28 15:53:23] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-28 15:53:23] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-28 15:53:23] Checking for Bowtie index files
[2014-04-28 15:53:23] Checking for reference FASTA file
[2014-04-28 15:53:23] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-28 15:53:25] Preparing reads
	 left reads: min. length=60, max. length=101, 21144214 kept reads (11500 discarded)
[2014-04-28 16:02:05] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-28 16:30:32] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-28 16:32:35] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-28 16:34:54] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-28 16:37:42] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-28 16:40:14] Searching for junctions via segment mapping
[2014-04-28 16:44:01] Retrieving sequences for splices
[2014-04-28 16:45:58] Indexing splices
[2014-04-28 16:46:44] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-28 16:47:36] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-28 16:48:38] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-28 16:49:40] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-28 16:50:41] Joining segment hits
[2014-04-28 16:53:53] Reporting output tracks
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[2014-04-28 17:05:55] Run complete: 01:12:32 elapsed