[2014-05-29 17:56:08] Beginning TopHat run (v2.0.8b)
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[2014-05-29 17:56:08] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-29 17:56:08] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-29 17:56:08] Checking for Bowtie index files
[2014-05-29 17:56:08] Checking for reference FASTA file
[2014-05-29 17:56:08] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-29 17:56:10] Preparing reads
	 left reads: min. length=60, max. length=101, 25449556 kept reads (1894 discarded)
[2014-05-29 18:07:14] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-29 18:48:11] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-29 18:52:13] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-29 18:56:29] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-29 19:00:53] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-29 19:05:15] Searching for junctions via segment mapping
[2014-05-29 19:49:09] Retrieving sequences for splices
[2014-05-29 19:51:15] Indexing splices
[2014-05-29 19:52:16] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-29 19:55:45] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-29 19:59:22] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-29 20:03:13] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-29 20:07:24] Joining segment hits
[2014-05-29 20:11:09] Reporting output tracks
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[2014-05-29 20:24:30] Run complete: 02:28:21 elapsed