[2014-05-28 13:36:46] Beginning TopHat run (v2.0.8b)
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[2014-05-28 13:36:46] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-28 13:36:46] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-28 13:36:46] Checking for Bowtie index files
[2014-05-28 13:36:46] Checking for reference FASTA file
[2014-05-28 13:36:46] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-28 13:36:49] Preparing reads
	 left reads: min. length=60, max. length=101, 27140093 kept reads (3497 discarded)
[2014-05-28 13:48:57] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-28 14:31:34] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-28 14:35:02] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-28 14:39:00] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-28 14:42:59] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-28 14:47:08] Searching for junctions via segment mapping
[2014-05-28 14:51:59] Retrieving sequences for splices
[2014-05-28 14:54:08] Indexing splices
[2014-05-28 14:55:00] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-28 14:56:41] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-28 14:58:46] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-28 15:00:55] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-28 15:02:51] Joining segment hits
[2014-05-28 15:06:31] Reporting output tracks
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[2014-05-28 15:22:30] Run complete: 01:45:44 elapsed