[2014-04-26 00:19:55] Beginning TopHat run (v2.0.8b)
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[2014-04-26 00:19:55] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-26 00:19:55] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-26 00:19:55] Checking for Bowtie index files
[2014-04-26 00:19:55] Checking for reference FASTA file
[2014-04-26 00:19:55] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-26 00:19:57] Preparing reads
	 left reads: min. length=60, max. length=101, 28291854 kept reads (10366 discarded)
[2014-04-26 00:31:20] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-26 01:07:48] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-26 01:10:35] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-26 01:13:48] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-26 01:17:45] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-26 01:21:06] Searching for junctions via segment mapping
[2014-04-26 01:25:22] Retrieving sequences for splices
[2014-04-26 01:27:18] Indexing splices
[2014-04-26 01:28:02] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-26 01:29:08] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-26 01:30:24] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-26 01:31:40] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-26 01:32:55] Joining segment hits
[2014-04-26 01:36:37] Reporting output tracks
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[2014-04-26 01:52:35] Run complete: 01:32:39 elapsed