[2014-05-24 21:27:10] Beginning TopHat run (v2.0.8b)
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[2014-05-24 21:27:10] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-24 21:27:10] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-24 21:27:10] Checking for Bowtie index files
[2014-05-24 21:27:10] Checking for reference FASTA file
[2014-05-24 21:27:10] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-24 21:27:12] Preparing reads
	 left reads: min. length=60, max. length=101, 24004125 kept reads (1991 discarded)
[2014-05-24 21:37:54] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-24 22:15:20] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-24 22:18:12] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-24 22:21:04] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-24 22:23:33] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-24 22:26:25] Searching for junctions via segment mapping
[2014-05-24 22:30:53] Retrieving sequences for splices
[2014-05-24 22:32:58] Indexing splices
[2014-05-24 22:33:37] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-24 22:35:10] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-24 22:37:01] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-24 22:38:54] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-24 22:40:32] Joining segment hits
[2014-05-24 22:43:59] Reporting output tracks
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[2014-05-24 22:56:41] Run complete: 01:29:31 elapsed