[2014-04-26 03:20:17] Beginning TopHat run (v2.0.8b)
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[2014-04-26 03:20:17] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-26 03:20:17] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-26 03:20:17] Checking for Bowtie index files
[2014-04-26 03:20:17] Checking for reference FASTA file
[2014-04-26 03:20:17] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-26 03:20:19] Preparing reads
	 left reads: min. length=60, max. length=101, 27314230 kept reads (10678 discarded)
[2014-04-26 03:31:21] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-26 04:06:40] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-26 04:09:12] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-26 04:12:06] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-26 04:15:18] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-26 04:18:34] Searching for junctions via segment mapping
[2014-04-26 04:22:45] Retrieving sequences for splices
[2014-04-26 04:24:42] Indexing splices
[2014-04-26 04:25:27] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-26 04:26:32] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-26 04:27:48] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-26 04:29:03] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-26 04:30:16] Joining segment hits
[2014-04-26 04:33:45] Reporting output tracks
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[2014-04-26 04:49:08] Run complete: 01:28:51 elapsed