[2014-05-28 11:55:48] Beginning TopHat run (v2.0.8b)
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[2014-05-28 11:55:48] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-28 11:55:48] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-28 11:55:48] Checking for Bowtie index files
[2014-05-28 11:55:48] Checking for reference FASTA file
[2014-05-28 11:55:48] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-28 11:56:01] Preparing reads
	 left reads: min. length=60, max. length=101, 25342938 kept reads (2176 discarded)
[2014-05-28 12:06:29] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-28 12:52:59] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-28 13:02:29] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-28 13:12:15] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-28 13:21:25] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-28 13:32:03] Searching for junctions via segment mapping
[2014-05-28 17:43:22] Retrieving sequences for splices
[2014-05-28 17:45:21] Indexing splices
[2014-05-28 17:46:34] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-28 18:04:41] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-28 18:22:54] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-28 18:41:38] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-28 19:01:54] Joining segment hits
[2014-05-28 19:08:59] Reporting output tracks
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[2014-05-28 19:25:39] Run complete: 07:29:51 elapsed