[2014-04-28 14:45:04] Beginning TopHat run (v2.0.8b)
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[2014-04-28 14:45:04] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-28 14:45:04] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-28 14:45:04] Checking for Bowtie index files
[2014-04-28 14:45:04] Checking for reference FASTA file
[2014-04-28 14:45:04] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-28 14:45:07] Preparing reads
	 left reads: min. length=60, max. length=101, 20122788 kept reads (11178 discarded)
[2014-04-28 14:53:17] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-28 15:19:51] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-28 15:21:44] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-28 15:23:53] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-28 15:26:28] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-28 15:28:49] Searching for junctions via segment mapping
[2014-04-28 15:32:22] Retrieving sequences for splices
[2014-04-28 15:34:19] Indexing splices
[2014-04-28 15:34:55] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-28 15:35:43] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-28 15:36:40] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-28 15:37:38] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-28 15:38:34] Joining segment hits
[2014-04-28 15:41:44] Reporting output tracks
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[2014-04-28 15:53:23] Run complete: 01:08:18 elapsed