[Mon Jun 14 14:29:14 2010] Beginning TopHat run (v1.0.13)
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[Mon Jun 14 14:29:14 2010] Preparing output location /projects/NBL/HS1194/311L9AAXX_8/tophat_wj/
[Mon Jun 14 14:29:14 2010] Checking for Bowtie index files
[Mon Jun 14 14:29:14 2010] Checking for reference FASTA file
[Mon Jun 14 14:29:14 2010] Checking for Bowtie
	Bowtie version:		 0.12.5.0
[Mon Jun 14 14:29:14 2010] Checking reads
	seed length:	 50bp
	format:		 fastq
	quality scale:	 phred33 (default)
[Mon Jun 14 14:31:31 2010] Reading known junctions from GFF file
[Mon Jun 14 14:36:14 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 15:49:41 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 15:59:57 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 16:41:27 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 17:22:53 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 18:20:18 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 18:25:39 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 19:18:14 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 20:08:29 2010] Searching for junctions via segment mapping
[Mon Jun 14 20:33:17 2010] Retrieving sequences for splices
[Mon Jun 14 20:36:17 2010] Indexing splices
[Mon Jun 14 20:46:38 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 21:00:58 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 21:14:46 2010] Joining segment hits
[Mon Jun 14 21:21:44 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 21:39:09 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 21:56:03 2010] Joining segment hits
[Mon Jun 14 22:08:26 2010] Reporting output tracks
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Run complete [08:55:03 elapsed]