[2014-04-29 17:01:39] Beginning TopHat run (v2.0.8b)
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[2014-04-29 17:01:39] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-29 17:01:39] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-29 17:01:39] Checking for Bowtie index files
[2014-04-29 17:01:39] Checking for reference FASTA file
[2014-04-29 17:01:39] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-29 17:01:43] Preparing reads
	 left reads: min. length=60, max. length=101, 18716679 kept reads (8387 discarded)
[2014-04-29 17:09:14] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-29 17:32:02] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-29 17:33:53] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-29 17:35:56] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-29 17:38:27] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-29 17:41:04] Searching for junctions via segment mapping
[2014-04-29 17:44:56] Retrieving sequences for splices
[2014-04-29 17:46:59] Indexing splices
[2014-04-29 17:47:35] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-29 17:48:31] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-29 17:49:38] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-29 17:50:46] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-29 17:51:54] Joining segment hits
[2014-04-29 17:55:19] Reporting output tracks
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[2014-04-29 18:07:21] Run complete: 01:05:41 elapsed