[2014-05-27 15:59:11] Beginning TopHat run (v2.0.8b)
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[2014-05-27 15:59:11] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-05-27 15:59:11] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-05-27 15:59:11] Checking for Bowtie index files
[2014-05-27 15:59:11] Checking for reference FASTA file
[2014-05-27 15:59:11] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-05-27 15:59:14] Preparing reads
	 left reads: min. length=60, max. length=101, 23351869 kept reads (991 discarded)
[2014-05-27 16:09:32] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-05-27 16:47:34] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-05-27 16:51:11] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-05-27 16:55:00] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-05-27 16:58:58] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-05-27 17:03:30] Searching for junctions via segment mapping
[2014-05-27 17:09:38] Retrieving sequences for splices
[2014-05-27 17:11:46] Indexing splices
[2014-05-27 17:12:18] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-05-27 17:16:14] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-05-27 17:20:35] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-05-27 17:24:47] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-05-27 17:29:18] Joining segment hits
[2014-05-27 17:34:09] Reporting output tracks
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[2014-05-27 17:48:26] Run complete: 01:49:14 elapsed