[2014-05-05 13:10:16] Beginning TopHat run (v2.0.8b)
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[2014-05-05 13:10:16] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-05 13:10:16] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-05 13:10:16] Checking for Bowtie index files
[2014-05-05 13:10:16] Checking for reference FASTA file
[2014-05-05 13:10:16] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-05 13:10:19] Preparing reads
	 left reads: min. length=60, max. length=101, 32669774 kept reads (7514 discarded)
[2014-05-05 13:23:52] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-05 14:03:38] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-05 14:07:26] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-05 14:11:30] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-05 14:16:35] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-05 14:21:18] Searching for junctions via segment mapping
[2014-05-05 14:27:51] Retrieving sequences for splices
[2014-05-05 14:29:49] Indexing splices
[2014-05-05 14:30:55] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-05 14:32:40] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-05 14:34:48] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-05 14:36:55] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-05 14:38:56] Joining segment hits
[2014-05-05 14:43:34] Reporting output tracks
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[2014-05-05 15:02:16] Run complete: 01:51:59 elapsed