[Mon Jun 14 16:15:42 2010] Beginning TopHat run (v1.0.13)
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[Mon Jun 14 16:15:42 2010] Preparing output location /projects/NBL/HS1197/302NNAAXX_7/tophat_wj/
[Mon Jun 14 16:15:44 2010] Checking for Bowtie index files
[Mon Jun 14 16:15:47 2010] Checking for reference FASTA file
[Mon Jun 14 16:15:47 2010] Checking for Bowtie
	Bowtie version:		 0.12.5.0
[Mon Jun 14 16:15:48 2010] Checking reads
	seed length:	 50bp
	format:		 fastq
	quality scale:	 phred33 (default)
[Mon Jun 14 16:21:10 2010] Reading known junctions from GFF file
[Mon Jun 14 16:58:34 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 18:53:16 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 19:03:19 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 19:38:48 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 20:13:42 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 21:33:40 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 21:37:12 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 22:25:43 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 23:11:58 2010] Searching for junctions via segment mapping
[Mon Jun 14 23:56:46 2010] Retrieving sequences for splices
[Tue Jun 15 00:00:53 2010] Indexing splices
[Tue Jun 15 00:26:00 2010] Mapping reads against segment_juncs with Bowtie
[Tue Jun 15 00:45:58 2010] Mapping reads against segment_juncs with Bowtie
[Tue Jun 15 01:03:34 2010] Joining segment hits
[Tue Jun 15 01:08:36 2010] Mapping reads against segment_juncs with Bowtie
[Tue Jun 15 01:34:11 2010] Mapping reads against segment_juncs with Bowtie
[Tue Jun 15 01:57:54 2010] Joining segment hits
[Tue Jun 15 02:02:51 2010] Reporting output tracks
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Run complete [10:07:07 elapsed]