[2014-04-27 12:21:02] Beginning TopHat run (v2.0.8b)
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[2014-04-27 12:21:02] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-27 12:21:02] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-27 12:21:02] Checking for Bowtie index files
[2014-04-27 12:21:02] Checking for reference FASTA file
[2014-04-27 12:21:02] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-27 12:21:04] Preparing reads
	 left reads: min. length=60, max. length=101, 16775282 kept reads (7936 discarded)
[2014-04-27 12:27:57] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-27 12:48:45] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-27 12:50:37] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-27 12:52:38] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-27 12:55:06] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-27 12:57:33] Searching for junctions via segment mapping
[2014-04-27 13:02:01] Retrieving sequences for splices
[2014-04-27 13:03:57] Indexing splices
[2014-04-27 13:04:46] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-27 13:05:42] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-27 13:06:48] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-27 13:07:55] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-27 13:09:00] Joining segment hits
[2014-04-27 13:12:12] Reporting output tracks
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[2014-04-27 13:22:24] Run complete: 01:01:21 elapsed