[2014-05-29 18:11:53] Beginning TopHat run (v2.0.8b)
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[2014-05-29 18:11:53] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-29 18:11:53] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-29 18:11:53] Checking for Bowtie index files
[2014-05-29 18:11:53] Checking for reference FASTA file
[2014-05-29 18:11:53] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-29 18:11:56] Preparing reads
	 left reads: min. length=60, max. length=101, 32623612 kept reads (358 discarded)
[2014-05-29 18:27:53] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-29 19:13:34] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-29 19:18:31] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-29 19:23:45] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-29 19:29:10] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-29 19:35:00] Searching for junctions via segment mapping
[2014-05-29 19:41:10] Retrieving sequences for splices
[2014-05-29 19:43:26] Indexing splices
[2014-05-29 19:44:38] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-29 19:47:12] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-29 19:50:09] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-29 19:53:06] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-29 19:55:54] Joining segment hits
[2014-05-29 20:00:56] Reporting output tracks
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[2014-05-29 20:18:31] Run complete: 02:06:37 elapsed