[2014-04-26 19:38:48] Beginning TopHat run (v2.0.8b)
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[2014-04-26 19:38:48] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-26 19:38:48] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-26 19:38:48] Checking for Bowtie index files
[2014-04-26 19:38:48] Checking for reference FASTA file
[2014-04-26 19:38:48] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-26 19:38:51] Preparing reads
	 left reads: min. length=60, max. length=101, 24730877 kept reads (7295 discarded)
[2014-04-26 19:48:47] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-26 20:18:20] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-26 20:20:39] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-26 20:23:12] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-26 20:25:59] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-26 20:29:02] Searching for junctions via segment mapping
[2014-04-26 20:33:05] Retrieving sequences for splices
[2014-04-26 20:35:07] Indexing splices
[2014-04-26 20:35:45] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-26 20:36:56] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-26 20:38:18] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-26 20:39:41] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-26 20:41:01] Joining segment hits
[2014-04-26 20:44:42] Reporting output tracks
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[2014-04-26 21:00:05] Run complete: 01:21:16 elapsed