[2014-05-29 15:10:57] Beginning TopHat run (v2.0.8b)
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[2014-05-29 15:10:57] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-29 15:10:57] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-29 15:10:57] Checking for Bowtie index files
[2014-05-29 15:10:57] Checking for reference FASTA file
[2014-05-29 15:10:57] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-29 15:11:00] Preparing reads
	 left reads: min. length=60, max. length=101, 21562547 kept reads (961 discarded)
[2014-05-29 15:21:08] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-29 15:51:25] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-29 15:57:08] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-29 16:02:04] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-29 16:06:45] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-29 16:11:39] Searching for junctions via segment mapping
[2014-05-29 16:58:06] Retrieving sequences for splices
[2014-05-29 17:00:05] Indexing splices
[2014-05-29 17:00:54] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-29 17:15:17] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-29 17:28:12] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-29 17:40:09] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-29 17:53:35] Joining segment hits
[2014-05-29 18:00:08] Reporting output tracks
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[2014-05-29 18:11:40] Run complete: 03:00:43 elapsed