[Mon Jun 14 15:19:10 2010] Beginning TopHat run (v1.0.13)
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[Mon Jun 14 15:19:10 2010] Preparing output location /projects/NBL/HS1197/311NGAAXX_2/tophat_wj/
[Mon Jun 14 15:19:10 2010] Checking for Bowtie index files
[Mon Jun 14 15:19:10 2010] Checking for reference FASTA file
[Mon Jun 14 15:19:10 2010] Checking for Bowtie
	Bowtie version:		 0.12.5.0
[Mon Jun 14 15:19:10 2010] Checking reads
	seed length:	 50bp
	format:		 fastq
	quality scale:	 phred33 (default)
[Mon Jun 14 15:23:06 2010] Reading known junctions from GFF file
[Mon Jun 14 15:34:00 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 17:25:46 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 17:33:08 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 17:57:37 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 18:22:18 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 20:07:57 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 20:13:28 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 20:43:52 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 21:13:57 2010] Searching for junctions via segment mapping
[Mon Jun 14 21:32:40 2010] Retrieving sequences for splices
[Mon Jun 14 21:35:45 2010] Indexing splices
[Mon Jun 14 21:49:03 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 22:03:24 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 22:16:53 2010] Joining segment hits
[Mon Jun 14 22:30:52 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 22:47:19 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 23:02:00 2010] Joining segment hits
[Mon Jun 14 23:13:21 2010] Reporting output tracks
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Run complete [10:09:44 elapsed]