[Mon Jun 14 14:47:24 2010] Beginning TopHat run (v1.0.13)
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[Mon Jun 14 14:47:24 2010] Preparing output location /projects/NBL/HS1195/30TTYAAXX_2/tophat_wj/
[Mon Jun 14 14:47:24 2010] Checking for Bowtie index files
[Mon Jun 14 14:47:24 2010] Checking for reference FASTA file
[Mon Jun 14 14:47:24 2010] Checking for Bowtie
	Bowtie version:		 0.12.5.0
[Mon Jun 14 14:47:25 2010] Checking reads
	seed length:	 50bp
	format:		 fastq
	quality scale:	 phred33 (default)
[Mon Jun 14 14:50:25 2010] Reading known junctions from GFF file
[Mon Jun 14 15:03:36 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 17:15:02 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 17:26:21 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 18:03:16 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 18:38:27 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 19:33:43 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 19:37:04 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 19:59:00 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 21:27:33 2010] Searching for junctions via segment mapping
[Mon Jun 14 22:48:34 2010] Retrieving sequences for splices
[Mon Jun 14 22:53:31 2010] Indexing splices
[Mon Jun 14 23:29:27 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 23:53:00 2010] Mapping reads against segment_juncs with Bowtie
[Tue Jun 15 00:13:19 2010] Joining segment hits
[Tue Jun 15 00:19:32 2010] Mapping reads against segment_juncs with Bowtie
[Tue Jun 15 00:38:19 2010] Mapping reads against segment_juncs with Bowtie
[Tue Jun 15 01:24:56 2010] Joining segment hits
[Tue Jun 15 01:29:50 2010] Reporting output tracks
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Run complete [11:01:26 elapsed]