[2014-05-29 12:59:08] Beginning TopHat run (v2.0.8b)
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[2014-05-29 12:59:08] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-29 12:59:08] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-29 12:59:08] Checking for Bowtie index files
[2014-05-29 12:59:08] Checking for reference FASTA file
[2014-05-29 12:59:08] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-29 12:59:10] Preparing reads
	 left reads: min. length=60, max. length=101, 26749087 kept reads (757 discarded)
[2014-05-29 13:11:18] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-29 13:51:25] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-29 13:54:31] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-29 13:57:54] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-29 14:01:20] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-29 14:04:58] Searching for junctions via segment mapping
[2014-05-29 14:10:14] Retrieving sequences for splices
[2014-05-29 14:12:20] Indexing splices
[2014-05-29 14:13:05] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-29 14:14:31] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-29 14:16:12] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-29 14:17:54] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-29 14:19:24] Joining segment hits
[2014-05-29 14:23:33] Reporting output tracks
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[2014-05-29 14:39:54] Run complete: 01:40:45 elapsed