[2014-05-27 17:17:51] Beginning TopHat run (v2.0.8b)
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[2014-05-27 17:17:51] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-27 17:17:51] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-27 17:17:51] Checking for Bowtie index files
[2014-05-27 17:17:51] Checking for reference FASTA file
[2014-05-27 17:17:51] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-27 17:17:54] Preparing reads
	 left reads: min. length=60, max. length=101, 26897206 kept reads (3000 discarded)
[2014-05-27 17:29:43] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-27 18:14:57] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-27 18:18:05] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-27 18:21:30] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-27 18:25:04] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-27 18:28:36] Searching for junctions via segment mapping
[2014-05-27 18:33:17] Retrieving sequences for splices
[2014-05-27 18:35:27] Indexing splices
[2014-05-27 18:36:17] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-27 18:37:49] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-27 18:39:40] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-27 18:41:35] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-27 18:43:20] Joining segment hits
[2014-05-27 18:46:54] Reporting output tracks
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[2014-05-27 19:03:11] Run complete: 01:45:19 elapsed