[2014-05-29 16:23:54] Beginning TopHat run (v2.0.8b)
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[2014-05-29 16:23:54] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-29 16:23:54] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-29 16:23:54] Checking for Bowtie index files
[2014-05-29 16:23:54] Checking for reference FASTA file
[2014-05-29 16:23:54] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-29 16:23:57] Preparing reads
	 left reads: min. length=60, max. length=101, 21622097 kept reads (2223 discarded)
[2014-05-29 16:34:24] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-29 17:08:06] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-29 17:10:42] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-29 17:13:26] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-29 17:16:15] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-29 17:19:14] Searching for junctions via segment mapping
[2014-05-29 17:46:30] Retrieving sequences for splices
[2014-05-29 17:48:41] Indexing splices
[2014-05-29 17:49:30] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-29 17:52:11] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-29 17:54:58] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-29 17:57:35] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-29 18:00:06] Joining segment hits
[2014-05-29 18:04:01] Reporting output tracks
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[2014-05-29 18:17:06] Run complete: 01:53:11 elapsed