[Mon Jun 14 15:21:47 2010] Beginning TopHat run (v1.0.13)
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[Mon Jun 14 15:21:47 2010] Preparing output location /projects/NBL/HS1197/311NGAAXX_5/tophat_wj/
[Mon Jun 14 15:21:47 2010] Checking for Bowtie index files
[Mon Jun 14 15:21:47 2010] Checking for reference FASTA file
[Mon Jun 14 15:21:47 2010] Checking for Bowtie
	Bowtie version:		 0.12.5.0
[Mon Jun 14 15:21:47 2010] Checking reads
	seed length:	 50bp
	format:		 fastq
	quality scale:	 phred33 (default)
[Mon Jun 14 15:25:35 2010] Reading known junctions from GFF file
[Mon Jun 14 15:35:19 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 17:20:48 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 17:28:10 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 17:53:12 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 18:17:43 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 19:59:14 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 20:04:48 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 20:33:55 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 21:01:59 2010] Searching for junctions via segment mapping
[Mon Jun 14 21:20:01 2010] Retrieving sequences for splices
[Mon Jun 14 21:23:04 2010] Indexing splices
[Mon Jun 14 21:36:26 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 21:50:32 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 22:03:19 2010] Joining segment hits
[Mon Jun 14 22:15:20 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 22:31:53 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 22:46:36 2010] Joining segment hits
[Mon Jun 14 22:55:52 2010] Reporting output tracks
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Run complete [09:48:56 elapsed]