[Mon Jun 14 15:19:22 2010] Beginning TopHat run (v1.0.13)
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[Mon Jun 14 15:19:22 2010] Preparing output location /projects/NBL/HS1198/30UBRAAXX_7/tophat_wj/
[Mon Jun 14 15:19:22 2010] Checking for Bowtie index files
[Mon Jun 14 15:19:22 2010] Checking for reference FASTA file
[Mon Jun 14 15:19:22 2010] Checking for Bowtie
	Bowtie version:		 0.12.5.0
[Mon Jun 14 15:19:22 2010] Checking reads
	seed length:	 50bp
	format:		 fastq
	quality scale:	 phred33 (default)
[Mon Jun 14 15:22:08 2010] Reading known junctions from GFF file
[Mon Jun 14 15:29:00 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 16:37:47 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 16:44:04 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 17:22:56 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 17:58:48 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 19:02:05 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 19:05:59 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 19:48:02 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 20:28:03 2010] Searching for junctions via segment mapping
[Mon Jun 14 20:53:33 2010] Retrieving sequences for splices
[Mon Jun 14 20:56:29 2010] Indexing splices
[Mon Jun 14 21:05:54 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 21:20:22 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 21:33:49 2010] Joining segment hits
[Mon Jun 14 21:40:03 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 21:55:52 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 22:10:44 2010] Joining segment hits
[Mon Jun 14 22:18:57 2010] Reporting output tracks
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Run complete [08:14:42 elapsed]