[Mon Jun 14 15:17:57 2010] Beginning TopHat run (v1.0.13)
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[Mon Jun 14 15:17:57 2010] Preparing output location /projects/NBL/HS1196/302NNAAXX_6/tophat_wj/
[Mon Jun 14 15:17:57 2010] Checking for Bowtie index files
[Mon Jun 14 15:17:57 2010] Checking for reference FASTA file
[Mon Jun 14 15:17:57 2010] Checking for Bowtie
	Bowtie version:		 0.12.5.0
[Mon Jun 14 15:17:57 2010] Checking reads
	seed length:	 50bp
	format:		 fastq
	quality scale:	 phred33 (default)
[Mon Jun 14 15:21:46 2010] Reading known junctions from GFF file
[Mon Jun 14 15:31:44 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 16:41:17 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 16:49:25 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 17:35:03 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 18:09:33 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 19:09:48 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 19:16:47 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 20:06:17 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 20:54:46 2010] Searching for junctions via segment mapping
[Mon Jun 14 21:39:54 2010] Retrieving sequences for splices
[Mon Jun 14 21:44:55 2010] Indexing splices
[Mon Jun 14 22:07:40 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 22:34:55 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 23:00:20 2010] Joining segment hits
[Mon Jun 14 23:16:40 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 23:47:54 2010] Mapping reads against segment_juncs with Bowtie
[Tue Jun 15 00:14:07 2010] Joining segment hits
[Tue Jun 15 00:28:23 2010] Reporting output tracks
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Run complete [09:52:31 elapsed]