[2014-04-30 09:42:20] Beginning TopHat run (v2.0.8b)
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[2014-04-30 09:42:20] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-30 09:42:20] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-30 09:42:20] Checking for Bowtie index files
[2014-04-30 09:42:20] Checking for reference FASTA file
[2014-04-30 09:42:20] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-30 09:42:22] Preparing reads
	 left reads: min. length=60, max. length=101, 20687165 kept reads (10199 discarded)
[2014-04-30 09:50:45] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-30 10:16:35] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-30 10:18:39] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-30 10:20:58] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-30 10:23:46] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-30 10:26:32] Searching for junctions via segment mapping
[2014-04-30 10:31:29] Retrieving sequences for splices
[2014-04-30 10:33:24] Indexing splices
[2014-04-30 10:33:59] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-30 10:34:57] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-30 10:36:08] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-30 10:37:19] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-30 10:38:27] Joining segment hits
[2014-04-30 10:41:48] Reporting output tracks
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[2014-04-30 10:53:58] Run complete: 01:11:37 elapsed