[2014-05-01 12:47:59] Beginning TopHat run (v2.0.8b)
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[2014-05-01 12:47:59] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-01 12:47:59] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-01 12:47:59] Checking for Bowtie index files
[2014-05-01 12:47:59] Checking for reference FASTA file
[2014-05-01 12:47:59] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-01 12:48:01] Preparing reads
	 left reads: min. length=60, max. length=101, 19106700 kept reads (9674 discarded)
[2014-05-01 12:55:41] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-01 13:26:11] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-01 13:32:45] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-01 13:39:48] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-01 13:46:45] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-01 13:54:47] Searching for junctions via segment mapping
[2014-05-01 20:26:58] Retrieving sequences for splices
[2014-05-01 20:28:55] Indexing splices
[2014-05-01 20:30:05] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-01 20:41:19] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-01 20:52:48] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-01 21:04:23] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-01 21:16:10] Joining segment hits
[2014-05-01 21:26:16] Reporting output tracks
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[2014-05-01 21:40:58] Run complete: 08:52:58 elapsed