[2014-05-24 20:34:31] Beginning TopHat run (v2.0.8b)
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[2014-05-24 20:34:31] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-24 20:34:31] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-24 20:34:31] Checking for Bowtie index files
[2014-05-24 20:34:31] Checking for reference FASTA file
[2014-05-24 20:34:31] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-24 20:34:33] Preparing reads
	 left reads: min. length=60, max. length=101, 20469739 kept reads (975 discarded)
[2014-05-24 20:42:56] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-24 21:14:59] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-24 21:17:00] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-24 21:19:08] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-24 21:21:24] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-24 21:24:01] Searching for junctions via segment mapping
[2014-05-24 21:29:36] Retrieving sequences for splices
[2014-05-24 21:31:43] Indexing splices
[2014-05-24 21:32:28] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-24 21:33:47] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-24 21:35:21] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-24 21:36:41] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-24 21:37:45] Joining segment hits
[2014-05-24 21:41:02] Reporting output tracks
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[2014-05-24 21:53:28] Run complete: 01:18:56 elapsed