[2014-04-29 20:47:29] Beginning TopHat run (v2.0.8b)
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[2014-04-29 20:47:29] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-29 20:47:29] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-29 20:47:29] Checking for Bowtie index files
[2014-04-29 20:47:29] Checking for reference FASTA file
[2014-04-29 20:47:29] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-29 20:47:31] Preparing reads
	 left reads: min. length=60, max. length=101, 21496616 kept reads (9816 discarded)
[2014-04-29 20:56:07] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-29 21:22:40] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-29 21:25:04] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-29 21:27:44] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-29 21:32:27] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-29 21:35:20] Searching for junctions via segment mapping
[2014-04-29 21:39:13] Retrieving sequences for splices
[2014-04-29 21:41:08] Indexing splices
[2014-04-29 21:41:42] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-29 21:42:46] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-29 21:44:04] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-29 21:45:24] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-29 21:46:37] Joining segment hits
[2014-04-29 21:50:20] Reporting output tracks
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[2014-04-29 22:03:30] Run complete: 01:16:00 elapsed