[2014-04-29 19:26:58] Beginning TopHat run (v2.0.8b)
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[2014-04-29 19:26:58] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-29 19:26:58] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-29 19:26:58] Checking for Bowtie index files
[2014-04-29 19:26:58] Checking for reference FASTA file
[2014-04-29 19:26:58] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-29 19:27:01] Preparing reads
	 left reads: min. length=60, max. length=101, 22080427 kept reads (9801 discarded)
[2014-04-29 19:35:51] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-29 20:03:58] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-29 20:06:33] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-29 20:09:23] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-29 20:14:40] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-29 20:17:46] Searching for junctions via segment mapping
[2014-04-29 20:21:51] Retrieving sequences for splices
[2014-04-29 20:23:48] Indexing splices
[2014-04-29 20:24:23] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-29 20:25:33] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-29 20:26:59] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-29 20:28:27] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-29 20:29:50] Joining segment hits
[2014-04-29 20:33:46] Reporting output tracks
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[2014-04-29 20:47:29] Run complete: 01:20:30 elapsed