[2014-05-27 13:47:00] Beginning TopHat run (v2.0.8b)
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[2014-05-27 13:47:00] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-27 13:47:00] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-27 13:47:00] Checking for Bowtie index files
[2014-05-27 13:47:00] Checking for reference FASTA file
[2014-05-27 13:47:00] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-27 13:47:02] Preparing reads
	 left reads: min. length=60, max. length=101, 24773035 kept reads (199 discarded)
[2014-05-27 13:57:02] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-27 14:37:46] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-27 14:40:15] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-27 14:42:52] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-27 14:45:38] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-27 14:48:31] Searching for junctions via segment mapping
[2014-05-27 14:53:34] Retrieving sequences for splices
[2014-05-27 14:55:41] Indexing splices
[2014-05-27 14:56:17] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-27 14:58:11] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-27 15:00:21] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-27 15:02:37] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-27 15:04:44] Joining segment hits
[2014-05-27 15:09:02] Reporting output tracks
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[2014-05-27 15:24:53] Run complete: 01:37:53 elapsed