[Mon Jun 14 14:45:13 2010] Beginning TopHat run (v1.0.13)
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[Mon Jun 14 14:45:13 2010] Preparing output location /projects/NBL/HS1196/3153YAAXX_3/tophat_wj/
[Mon Jun 14 14:45:13 2010] Checking for Bowtie index files
[Mon Jun 14 14:45:13 2010] Checking for reference FASTA file
[Mon Jun 14 14:45:13 2010] Checking for Bowtie
	Bowtie version:		 0.12.5.0
[Mon Jun 14 14:45:13 2010] Checking reads
	seed length:	 50bp
	format:		 fastq
	quality scale:	 phred33 (default)
[Mon Jun 14 14:47:24 2010] Reading known junctions from GFF file
[Mon Jun 14 14:51:59 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 16:02:45 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 16:12:31 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 16:53:31 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 17:28:56 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 18:24:50 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 18:29:08 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 19:05:22 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 19:41:07 2010] Searching for junctions via segment mapping
[Mon Jun 14 20:00:08 2010] Retrieving sequences for splices
[Mon Jun 14 20:03:10 2010] Indexing splices
[Mon Jun 14 20:13:17 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 20:25:29 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 20:36:49 2010] Joining segment hits
[Mon Jun 14 20:42:36 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 20:56:52 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 21:10:14 2010] Joining segment hits
[Mon Jun 14 21:16:30 2010] Reporting output tracks
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Run complete [07:43:37 elapsed]