[2014-05-29 10:23:32] Beginning TopHat run (v2.0.8b)
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[2014-05-29 10:23:32] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-29 10:23:32] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-29 10:23:32] Checking for Bowtie index files
[2014-05-29 10:23:32] Checking for reference FASTA file
[2014-05-29 10:23:32] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-29 10:23:35] Preparing reads
	 left reads: min. length=60, max. length=101, 34624510 kept reads (184 discarded)
[2014-05-29 10:40:18] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-29 11:29:40] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-29 11:33:55] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-29 11:38:22] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-29 11:43:04] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-29 11:49:20] Searching for junctions via segment mapping
[2014-05-29 11:56:37] Retrieving sequences for splices
[2014-05-29 11:58:46] Indexing splices
[2014-05-29 12:00:17] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-29 12:03:16] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-29 12:06:53] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-29 12:10:31] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-29 12:13:32] Joining segment hits
[2014-05-29 12:17:47] Reporting output tracks
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[2014-05-29 12:35:57] Run complete: 02:12:25 elapsed