[2014-05-29 12:22:24] Beginning TopHat run (v2.0.8b)
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[2014-05-29 12:22:24] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-29 12:22:24] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-29 12:22:24] Checking for Bowtie index files
[2014-05-29 12:22:24] Checking for reference FASTA file
[2014-05-29 12:22:24] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-29 12:22:26] Preparing reads
	 left reads: min. length=60, max. length=101, 30746584 kept reads (672 discarded)
[2014-05-29 12:35:51] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-29 13:19:01] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-29 13:27:36] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-29 13:35:44] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-29 13:41:55] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-29 13:49:01] Searching for junctions via segment mapping
[2014-05-29 15:08:06] Retrieving sequences for splices
[2014-05-29 15:10:17] Indexing splices
[2014-05-29 15:11:37] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-29 15:36:58] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-29 16:00:41] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-29 16:22:17] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-29 16:46:46] Joining segment hits
[2014-05-29 16:59:14] Reporting output tracks
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[2014-05-29 17:15:04] Run complete: 04:52:39 elapsed