[2014-05-28 16:33:46] Beginning TopHat run (v2.0.8b)
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[2014-05-28 16:33:46] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-28 16:33:46] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-28 16:33:46] Checking for Bowtie index files
[2014-05-28 16:33:46] Checking for reference FASTA file
[2014-05-28 16:33:46] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-28 16:33:49] Preparing reads
	 left reads: min. length=60, max. length=101, 28180289 kept reads (2381 discarded)
[2014-05-28 16:46:18] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-28 17:28:58] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-28 17:32:30] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-28 17:36:30] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-28 17:40:13] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-28 17:43:25] Searching for junctions via segment mapping
[2014-05-28 17:48:20] Retrieving sequences for splices
[2014-05-28 17:50:25] Indexing splices
[2014-05-28 17:51:32] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-28 17:53:22] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-28 17:55:35] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-28 17:57:55] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-28 18:00:01] Joining segment hits
[2014-05-28 18:04:26] Reporting output tracks
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[2014-05-28 18:21:13] Run complete: 01:47:26 elapsed