[2014-05-28 17:03:44] Beginning TopHat run (v2.0.8b)
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[2014-05-28 17:03:44] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-28 17:03:44] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-28 17:03:44] Checking for Bowtie index files
[2014-05-28 17:03:44] Checking for reference FASTA file
[2014-05-28 17:03:44] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-28 17:03:46] Preparing reads
	 left reads: min. length=60, max. length=101, 24403012 kept reads (744 discarded)
[2014-05-28 17:14:48] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-28 17:53:33] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-28 17:57:25] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-28 18:01:37] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-28 18:05:54] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-28 18:10:44] Searching for junctions via segment mapping
[2014-05-28 18:16:57] Retrieving sequences for splices
[2014-05-28 18:19:04] Indexing splices
[2014-05-28 18:19:39] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-28 18:24:07] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-28 18:29:00] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-28 18:33:48] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-28 18:38:53] Joining segment hits
[2014-05-28 18:44:04] Reporting output tracks
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[2014-05-28 18:58:44] Run complete: 01:55:00 elapsed