[2014-05-27 13:45:40] Beginning TopHat run (v2.0.8b)
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[2014-05-27 13:45:40] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-27 13:45:40] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-27 13:45:40] Checking for Bowtie index files
[2014-05-27 13:45:40] Checking for reference FASTA file
[2014-05-27 13:45:40] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-27 13:45:42] Preparing reads
	 left reads: min. length=60, max. length=101, 27955363 kept reads (569 discarded)
[2014-05-27 13:57:02] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-27 14:40:22] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-27 14:42:58] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-27 14:45:51] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-27 14:49:03] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-27 14:52:48] Searching for junctions via segment mapping
[2014-05-27 14:59:16] Retrieving sequences for splices
[2014-05-27 15:01:20] Indexing splices
[2014-05-27 15:02:01] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-27 15:03:29] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-27 15:05:45] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-27 15:07:45] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-27 15:09:24] Joining segment hits
[2014-05-27 15:13:26] Reporting output tracks
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[2014-05-27 15:28:32] Run complete: 01:42:51 elapsed