[Mon Jun 14 15:21:00 2010] Beginning TopHat run (v1.0.13)
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[Mon Jun 14 15:21:00 2010] Preparing output location /projects/NBL/HS1198/30UBRAAXX_5/tophat_wj/
[Mon Jun 14 15:21:00 2010] Checking for Bowtie index files
[Mon Jun 14 15:21:01 2010] Checking for reference FASTA file
[Mon Jun 14 15:21:01 2010] Checking for Bowtie
	Bowtie version:		 0.12.5.0
[Mon Jun 14 15:21:01 2010] Checking reads
	seed length:	 50bp
	format:		 fastq
	quality scale:	 phred33 (default)
[Mon Jun 14 15:23:42 2010] Reading known junctions from GFF file
[Mon Jun 14 15:32:16 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 16:40:28 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 16:48:29 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 17:26:59 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 18:03:06 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 19:07:41 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 19:11:32 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 19:55:51 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 20:39:07 2010] Searching for junctions via segment mapping
[Mon Jun 14 21:06:59 2010] Retrieving sequences for splices
[Mon Jun 14 21:10:02 2010] Indexing splices
[Mon Jun 14 21:20:53 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 21:37:23 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 21:53:10 2010] Joining segment hits
[Mon Jun 14 22:02:32 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 22:20:19 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 22:36:36 2010] Joining segment hits
[Mon Jun 14 22:43:28 2010] Reporting output tracks
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Run complete [08:42:37 elapsed]