[Mon Jun 14 15:12:23 2010] Beginning TopHat run (v1.0.13)
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[Mon Jun 14 15:12:23 2010] Preparing output location /projects/NBL/HS1196/3153YAAXX_7/tophat_wj/
[Mon Jun 14 15:12:23 2010] Checking for Bowtie index files
[Mon Jun 14 15:12:23 2010] Checking for reference FASTA file
[Mon Jun 14 15:12:23 2010] Checking for Bowtie
	Bowtie version:		 0.12.5.0
[Mon Jun 14 15:12:23 2010] Checking reads
	seed length:	 50bp
	format:		 fastq
	quality scale:	 phred33 (default)
[Mon Jun 14 15:16:12 2010] Reading known junctions from GFF file
[Mon Jun 14 15:29:48 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 17:28:31 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 17:38:35 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 18:07:40 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 18:37:08 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 19:41:46 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 19:45:10 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 20:24:36 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 21:00:18 2010] Searching for junctions via segment mapping
[Mon Jun 14 21:19:03 2010] Retrieving sequences for splices
[Mon Jun 14 21:21:59 2010] Indexing splices
[Mon Jun 14 21:32:15 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 21:44:38 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 21:56:01 2010] Joining segment hits
[Mon Jun 14 22:08:26 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 22:22:57 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 22:36:48 2010] Joining segment hits
[Mon Jun 14 22:43:43 2010] Reporting output tracks
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Run complete [08:50:49 elapsed]