[2014-05-29 17:22:17] Beginning TopHat run (v2.0.8b)
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[2014-05-29 17:22:17] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-29 17:22:17] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-29 17:22:17] Checking for Bowtie index files
[2014-05-29 17:22:17] Checking for reference FASTA file
[2014-05-29 17:22:17] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-29 17:22:20] Preparing reads
	 left reads: min. length=60, max. length=101, 28308485 kept reads (973 discarded)
[2014-05-29 17:34:38] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-29 18:21:41] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-29 18:24:57] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-29 18:28:20] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-29 18:31:56] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-29 18:35:52] Searching for junctions via segment mapping
[2014-05-29 18:41:08] Retrieving sequences for splices
[2014-05-29 18:43:18] Indexing splices
[2014-05-29 18:43:56] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-29 18:46:13] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-29 18:48:35] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-29 18:50:50] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-29 18:53:16] Joining segment hits
[2014-05-29 18:56:51] Reporting output tracks
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[2014-05-29 19:12:07] Run complete: 01:49:49 elapsed