[Mon Jun 14 14:34:43 2010] Beginning TopHat run (v1.0.13)
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[Mon Jun 14 14:34:43 2010] Preparing output location /projects/NBL/HS1195/30TTYAAXX_3/tophat_wj/
[Mon Jun 14 14:34:43 2010] Checking for Bowtie index files
[Mon Jun 14 14:34:43 2010] Checking for reference FASTA file
[Mon Jun 14 14:34:43 2010] Checking for Bowtie
	Bowtie version:		 0.12.5.0
[Mon Jun 14 14:34:43 2010] Checking reads
	seed length:	 50bp
	format:		 fastq
	quality scale:	 phred33 (default)
[Mon Jun 14 14:37:12 2010] Reading known junctions from GFF file
[Mon Jun 14 14:41:52 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 15:47:23 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 16:03:26 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 16:32:49 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 16:59:57 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 17:49:15 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 17:53:08 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 18:16:51 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 19:13:58 2010] Searching for junctions via segment mapping
[Mon Jun 14 20:05:15 2010] Retrieving sequences for splices
[Mon Jun 14 20:08:46 2010] Indexing splices
[Mon Jun 14 20:32:23 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 20:53:04 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 21:11:30 2010] Joining segment hits
[Mon Jun 14 21:18:45 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 21:37:57 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 22:07:56 2010] Joining segment hits
[Mon Jun 14 22:14:57 2010] Reporting output tracks
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Run complete [08:58:28 elapsed]