[2014-04-26 13:35:39] Beginning TopHat run (v2.0.8b)
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[2014-04-26 13:35:39] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-26 13:35:39] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-26 13:35:39] Checking for Bowtie index files
[2014-04-26 13:35:39] Checking for reference FASTA file
[2014-04-26 13:35:39] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-26 13:35:42] Preparing reads
	 left reads: min. length=60, max. length=101, 27252531 kept reads (7849 discarded)
[2014-04-26 13:46:46] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-26 14:19:50] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-26 14:22:47] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-26 14:25:58] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-26 14:29:55] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-26 14:33:23] Searching for junctions via segment mapping
[2014-04-26 14:37:51] Retrieving sequences for splices
[2014-04-26 14:39:47] Indexing splices
[2014-04-26 14:40:26] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-26 14:41:51] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-26 14:43:28] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-26 14:45:05] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-26 14:46:39] Joining segment hits
[2014-04-26 14:50:51] Reporting output tracks
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[2014-04-26 15:07:26] Run complete: 01:31:47 elapsed