[2014-04-25 19:53:23] Beginning TopHat run (v2.0.8b)
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[2014-04-25 19:53:23] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-25 19:53:23] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-25 19:53:23] Checking for Bowtie index files
[2014-04-25 19:53:23] Checking for reference FASTA file
[2014-04-25 19:53:23] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-25 19:53:25] Preparing reads
	 left reads: min. length=60, max. length=101, 28146156 kept reads (8676 discarded)
[2014-04-25 20:04:45] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-25 20:40:46] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-25 20:43:39] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-25 20:46:50] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-25 20:50:48] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-25 20:54:08] Searching for junctions via segment mapping
[2014-04-25 20:58:23] Retrieving sequences for splices
[2014-04-25 21:00:19] Indexing splices
[2014-04-25 21:01:00] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-25 21:02:06] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-25 21:03:24] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-25 21:04:41] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-25 21:05:57] Joining segment hits
[2014-04-25 21:09:43] Reporting output tracks
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[2014-04-25 21:25:26] Run complete: 01:32:03 elapsed