[2014-04-28 17:05:56] Beginning TopHat run (v2.0.8b)
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[2014-04-28 17:05:56] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-28 17:05:56] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-28 17:05:56] Checking for Bowtie index files
[2014-04-28 17:05:56] Checking for reference FASTA file
[2014-04-28 17:05:56] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-28 17:06:10] Preparing reads
	 left reads: min. length=60, max. length=101, 17980073 kept reads (8259 discarded)
[2014-04-28 17:13:26] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-28 17:37:03] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-28 17:38:55] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-28 17:40:53] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-28 17:42:59] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-28 17:45:12] Searching for junctions via segment mapping
[2014-04-28 17:48:43] Retrieving sequences for splices
[2014-04-28 17:50:41] Indexing splices
[2014-04-28 17:51:24] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-28 17:52:09] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-28 17:53:03] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-28 17:53:58] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-28 17:55:02] Joining segment hits
[2014-04-28 17:59:15] Reporting output tracks
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[2014-04-28 18:14:21] Run complete: 01:08:25 elapsed