[2014-05-28 04:41:31] Beginning TopHat run (v2.0.8b)
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[2014-05-28 04:41:31] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-28 04:41:31] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-28 04:41:31] Checking for Bowtie index files
[2014-05-28 04:41:31] Checking for reference FASTA file
[2014-05-28 04:41:31] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-28 04:41:33] Preparing reads
	 left reads: min. length=60, max. length=101, 24008270 kept reads (2424 discarded)
[2014-05-28 04:52:06] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-28 05:25:10] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-28 05:27:44] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-28 05:30:35] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-28 05:33:28] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-28 05:36:22] Searching for junctions via segment mapping
[2014-05-28 05:41:45] Retrieving sequences for splices
[2014-05-28 05:43:41] Indexing splices
[2014-05-28 05:44:30] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-28 05:48:56] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-28 05:53:34] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-28 05:58:09] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-28 06:03:11] Joining segment hits
[2014-05-28 06:08:28] Reporting output tracks
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[2014-05-28 06:22:12] Run complete: 01:40:40 elapsed