[2014-04-30 02:59:32] Beginning TopHat run (v2.0.8b)
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[2014-04-30 02:59:32] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-30 02:59:32] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-30 02:59:32] Checking for Bowtie index files
[2014-04-30 02:59:32] Checking for reference FASTA file
[2014-04-30 02:59:32] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-30 02:59:35] Preparing reads
	 left reads: min. length=60, max. length=101, 19882449 kept reads (10741 discarded)
[2014-04-30 03:07:40] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-30 03:32:45] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-30 03:34:39] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-30 03:36:48] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-30 03:39:22] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-30 03:41:55] Searching for junctions via segment mapping
[2014-04-30 03:46:32] Retrieving sequences for splices
[2014-04-30 03:48:28] Indexing splices
[2014-04-30 03:49:08] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-30 03:50:02] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-30 03:51:07] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-30 03:52:12] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-30 03:53:14] Joining segment hits
[2014-04-30 03:56:27] Reporting output tracks
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[2014-04-30 04:08:14] Run complete: 01:08:41 elapsed