[2014-04-26 23:58:41] Beginning TopHat run (v2.0.8b)
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[2014-04-26 23:58:41] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-26 23:58:41] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-26 23:58:41] Checking for Bowtie index files
[2014-04-26 23:58:41] Checking for reference FASTA file
[2014-04-26 23:58:41] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-26 23:58:46] Preparing reads
	 left reads: min. length=60, max. length=101, 19524706 kept reads (17658 discarded)
[2014-04-27 00:06:42] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-27 00:36:27] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-27 00:38:29] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-27 00:41:00] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-27 00:43:47] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-27 00:46:12] Searching for junctions via segment mapping
[2014-04-27 00:55:05] Retrieving sequences for splices
[2014-04-27 00:57:02] Indexing splices
[2014-04-27 00:57:49] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-27 00:59:18] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-27 01:01:01] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-27 01:02:42] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-27 01:04:25] Joining segment hits
[2014-04-27 01:08:21] Reporting output tracks
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[2014-04-27 01:21:49] Run complete: 01:23:07 elapsed