[2014-05-05 18:52:14] Beginning TopHat run (v2.0.8b)
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[2014-05-05 18:52:14] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-05 18:52:14] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-05 18:52:14] Checking for Bowtie index files
[2014-05-05 18:52:14] Checking for reference FASTA file
[2014-05-05 18:52:14] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-05 18:52:30] Preparing reads
	 left reads: min. length=60, max. length=101, 30196862 kept reads (7302 discarded)
[2014-05-05 19:04:44] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-05 19:42:37] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-05 19:47:17] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-05 19:51:15] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-05 19:55:19] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-05 19:59:36] Searching for junctions via segment mapping
[2014-05-05 20:08:09] Retrieving sequences for splices
[2014-05-05 20:10:06] Indexing splices
[2014-05-05 20:10:40] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-05 20:14:01] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-05 20:17:39] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-05 20:21:13] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-05 20:25:00] Joining segment hits
[2014-05-05 20:32:36] Reporting output tracks
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[2014-05-05 20:52:43] Run complete: 02:00:28 elapsed