[Mon Jun 14 14:56:48 2010] Beginning TopHat run (v1.0.13)
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[Mon Jun 14 14:56:48 2010] Preparing output location /projects/NBL/HS1195/30TTYAAXX_4/tophat_wj/
[Mon Jun 14 14:56:48 2010] Checking for Bowtie index files
[Mon Jun 14 14:56:48 2010] Checking for reference FASTA file
[Mon Jun 14 14:56:48 2010] Checking for Bowtie
	Bowtie version:		 0.12.5.0
[Mon Jun 14 14:56:49 2010] Checking reads
	seed length:	 50bp
	format:		 fastq
	quality scale:	 phred33 (default)
[Mon Jun 14 15:00:03 2010] Reading known junctions from GFF file
[Mon Jun 14 15:10:50 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 16:44:14 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 17:03:23 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 17:43:11 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 18:18:42 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 19:21:50 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 19:25:47 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 20:01:46 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 21:02:16 2010] Searching for junctions via segment mapping
[Mon Jun 14 22:01:15 2010] Retrieving sequences for splices
[Mon Jun 14 22:05:50 2010] Indexing splices
[Mon Jun 14 22:35:17 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 23:00:26 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 23:21:32 2010] Joining segment hits
[Mon Jun 14 23:26:23 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 23:49:28 2010] Mapping reads against segment_juncs with Bowtie
[Tue Jun 15 00:20:48 2010] Joining segment hits
[Tue Jun 15 00:24:57 2010] Reporting output tracks
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Run complete [09:49:02 elapsed]