[Mon Jun 14 14:48:59 2010] Beginning TopHat run (v1.0.13)
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[Mon Jun 14 14:48:59 2010] Preparing output location /projects/NBL/HS1195/30TTYAAXX_6/tophat_wj/
[Mon Jun 14 14:48:59 2010] Checking for Bowtie index files
[Mon Jun 14 14:48:59 2010] Checking for reference FASTA file
[Mon Jun 14 14:48:59 2010] Checking for Bowtie
	Bowtie version:		 0.12.5.0
[Mon Jun 14 14:48:59 2010] Checking reads
	seed length:	 50bp
	format:		 fastq
	quality scale:	 phred33 (default)
[Mon Jun 14 14:51:52 2010] Reading known junctions from GFF file
[Mon Jun 14 15:02:12 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 16:41:53 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 16:53:18 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 17:24:03 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 17:51:32 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 18:21:24 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 18:27:42 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 18:43:02 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 19:44:09 2010] Searching for junctions via segment mapping
[Mon Jun 14 20:55:18 2010] Retrieving sequences for splices
[Mon Jun 14 20:59:11 2010] Indexing splices
[Mon Jun 14 21:22:01 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 21:42:08 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 21:59:27 2010] Joining segment hits
[Mon Jun 14 22:09:24 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 22:23:26 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 22:56:40 2010] Joining segment hits
[Mon Jun 14 23:02:01 2010] Reporting output tracks
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Run complete [09:29:18 elapsed]