[2014-05-27 15:25:05] Beginning TopHat run (v2.0.8b)
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[2014-05-27 15:25:05] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-27 15:25:05] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-27 15:25:05] Checking for Bowtie index files
[2014-05-27 15:25:05] Checking for reference FASTA file
[2014-05-27 15:25:05] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-27 15:25:09] Preparing reads
	 left reads: min. length=60, max. length=101, 27146260 kept reads (1542 discarded)
[2014-05-27 15:37:30] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-27 16:30:37] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-27 16:47:41] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-27 17:04:45] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-27 17:21:23] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-27 17:40:53] Searching for junctions via segment mapping
[2014-05-28 01:59:17] Retrieving sequences for splices
[2014-05-28 02:01:27] Indexing splices
[2014-05-28 02:03:17] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-28 02:37:15] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-28 03:11:44] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-28 03:46:11] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-28 04:19:31] Joining segment hits
[2014-05-28 04:29:58] Reporting output tracks
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[2014-05-28 04:48:26] Run complete: 13:23:20 elapsed