[2014-05-28 15:22:30] Beginning TopHat run (v2.0.8b)
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[2014-05-28 15:22:30] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-28 15:22:30] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-28 15:22:31] Checking for Bowtie index files
[2014-05-28 15:22:31] Checking for reference FASTA file
[2014-05-28 15:22:31] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-28 15:22:33] Preparing reads
	 left reads: min. length=60, max. length=101, 26605693 kept reads (4035 discarded)
[2014-05-28 15:34:24] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-28 16:14:42] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-28 16:18:04] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-28 16:21:54] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-28 16:25:48] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-28 16:29:48] Searching for junctions via segment mapping
[2014-05-28 16:34:22] Retrieving sequences for splices
[2014-05-28 16:36:28] Indexing splices
[2014-05-28 16:37:19] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-28 16:38:59] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-28 16:41:01] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-28 16:43:07] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-28 16:45:00] Joining segment hits
[2014-05-28 16:48:38] Reporting output tracks
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[2014-05-28 17:03:43] Run complete: 01:41:12 elapsed