[2014-05-29 18:17:06] Beginning TopHat run (v2.0.8b)
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[2014-05-29 18:17:06] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-29 18:17:06] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-29 18:17:06] Checking for Bowtie index files
[2014-05-29 18:17:06] Checking for reference FASTA file
[2014-05-29 18:17:06] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-29 18:17:08] Preparing reads
	 left reads: min. length=60, max. length=101, 26683130 kept reads (868 discarded)
[2014-05-29 18:28:57] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-29 19:10:19] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-29 19:14:16] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-29 19:18:25] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-29 19:22:38] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-29 19:26:23] Searching for junctions via segment mapping
[2014-05-29 19:53:53] Retrieving sequences for splices
[2014-05-29 19:55:56] Indexing splices
[2014-05-29 19:56:46] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-29 19:59:43] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-29 20:03:05] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-29 20:06:47] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-29 20:09:57] Joining segment hits
[2014-05-29 20:13:44] Reporting output tracks
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[2014-05-29 20:27:45] Run complete: 02:10:39 elapsed