[2014-05-05 16:56:48] Beginning TopHat run (v2.0.8b)
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[2014-05-05 16:56:48] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-05 16:56:48] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-05 16:56:48] Checking for Bowtie index files
[2014-05-05 16:56:48] Checking for reference FASTA file
[2014-05-05 16:56:48] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-05 16:56:58] Preparing reads
	 left reads: min. length=60, max. length=101, 30560878 kept reads (7106 discarded)
[2014-05-05 17:09:20] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-05 17:46:14] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-05 17:49:39] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-05 17:53:28] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-05 17:57:26] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-05 18:01:43] Searching for junctions via segment mapping
[2014-05-05 18:09:22] Retrieving sequences for splices
[2014-05-05 18:11:22] Indexing splices
[2014-05-05 18:11:56] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-05 18:15:21] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-05 18:19:06] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-05 18:22:46] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-05 18:26:38] Joining segment hits
[2014-05-05 18:33:13] Reporting output tracks
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[2014-05-05 18:52:14] Run complete: 01:55:25 elapsed