[Mon Jun 14 14:55:38 2010] Beginning TopHat run (v1.0.13)
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[Mon Jun 14 14:55:38 2010] Preparing output location /projects/NBL/HS1196/3153YAAXX_5/tophat_wj/
[Mon Jun 14 14:55:38 2010] Checking for Bowtie index files
[Mon Jun 14 14:55:38 2010] Checking for reference FASTA file
[Mon Jun 14 14:55:38 2010] Checking for Bowtie
	Bowtie version:		 0.12.5.0
[Mon Jun 14 14:55:38 2010] Checking reads
	seed length:	 50bp
	format:		 fastq
	quality scale:	 phred33 (default)
[Mon Jun 14 14:58:04 2010] Reading known junctions from GFF file
[Mon Jun 14 15:02:43 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 16:12:44 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 16:18:43 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 16:48:25 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 17:16:33 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 18:15:26 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 18:19:14 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 18:56:59 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 19:32:04 2010] Searching for junctions via segment mapping
[Mon Jun 14 19:50:32 2010] Retrieving sequences for splices
[Mon Jun 14 19:53:28 2010] Indexing splices
[Mon Jun 14 20:03:18 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 20:15:16 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 20:26:36 2010] Joining segment hits
[Mon Jun 14 20:33:18 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 20:47:22 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 21:00:20 2010] Joining segment hits
[Mon Jun 14 21:05:20 2010] Reporting output tracks
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Run complete [07:26:40 elapsed]