[2014-04-29 14:28:42] Beginning TopHat run (v2.0.8b)
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[2014-04-29 14:28:42] Checking for Bowtie
		  Bowtie version:	 2.1.0.0
[2014-04-29 14:28:42] Checking for Samtools
		Samtools version:	 0.1.19.0
[2014-04-29 14:28:42] Checking for Bowtie index files
[2014-04-29 14:28:42] Checking for reference FASTA file
[2014-04-29 14:28:42] Generating SAM header for /home/rneme/PopTranscriptomes/mapping/index/mm10
	format:		 fastq
	quality scale:	 phred33 (default)
[2014-04-29 14:28:48] Preparing reads
	 left reads: min. length=60, max. length=101, 22570019 kept reads (10127 discarded)
[2014-04-29 14:38:23] Mapping left_kept_reads to genome mm10 with Bowtie2 
[2014-04-29 15:06:23] Mapping left_kept_reads_seg1 to genome mm10 with Bowtie2 (1/4)
[2014-04-29 15:08:32] Mapping left_kept_reads_seg2 to genome mm10 with Bowtie2 (2/4)
[2014-04-29 15:10:56] Mapping left_kept_reads_seg3 to genome mm10 with Bowtie2 (3/4)
[2014-04-29 15:13:44] Mapping left_kept_reads_seg4 to genome mm10 with Bowtie2 (4/4)
[2014-04-29 15:16:40] Searching for junctions via segment mapping
[2014-04-29 15:20:45] Retrieving sequences for splices
[2014-04-29 15:22:42] Indexing splices
[2014-04-29 15:23:19] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2014-04-29 15:24:27] Mapping left_kept_reads_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2014-04-29 15:25:46] Mapping left_kept_reads_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2014-04-29 15:27:05] Mapping left_kept_reads_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2014-04-29 15:28:25] Joining segment hits
[2014-04-29 15:32:07] Reporting output tracks
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[2014-04-29 15:46:08] Run complete: 01:17:26 elapsed