[2014-04-28 19:33:17] Beginning TopHat run (v2.0.8b)
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[2014-04-28 19:33:17] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-28 19:33:17] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-28 19:33:17] Checking for Bowtie index files
[2014-04-28 19:33:17] Checking for reference FASTA file
[2014-04-28 19:33:17] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-28 19:33:20] Preparing reads
	 left reads: min. length=60, max. length=101, 19023660 kept reads (10070 discarded)
[2014-04-28 19:41:02] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-28 20:06:46] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-28 20:08:37] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-28 20:10:43] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-28 20:13:15] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-28 20:15:36] Searching for junctions via segment mapping
[2014-04-28 20:19:12] Retrieving sequences for splices
[2014-04-28 20:21:09] Indexing splices
[2014-04-28 20:21:47] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-28 20:22:36] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-28 20:23:33] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-28 20:24:30] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-28 20:25:25] Joining segment hits
[2014-04-28 20:28:38] Reporting output tracks
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[2014-04-28 20:40:05] Run complete: 01:06:47 elapsed