[Mon Jun 14 15:09:41 2010] Beginning TopHat run (v1.0.13)
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[Mon Jun 14 15:09:41 2010] Preparing output location /projects/NBL/HS1198/30UBRAAXX_3/tophat_wj/
[Mon Jun 14 15:09:41 2010] Checking for Bowtie index files
[Mon Jun 14 15:09:41 2010] Checking for reference FASTA file
[Mon Jun 14 15:09:41 2010] Checking for Bowtie
	Bowtie version:		 0.12.5.0
[Mon Jun 14 15:09:41 2010] Checking reads
	seed length:	 50bp
	format:		 fastq
	quality scale:	 phred33 (default)
[Mon Jun 14 15:12:06 2010] Reading known junctions from GFF file
[Mon Jun 14 15:20:43 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 16:31:18 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 16:40:36 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 17:23:12 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 18:01:20 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 19:05:28 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 19:08:58 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 19:56:47 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 20:41:13 2010] Searching for junctions via segment mapping
[Mon Jun 14 21:13:33 2010] Retrieving sequences for splices
[Mon Jun 14 21:16:31 2010] Indexing splices
[Mon Jun 14 21:28:17 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 21:46:07 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 22:02:11 2010] Joining segment hits
[Mon Jun 14 22:11:11 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 22:31:08 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 22:48:27 2010] Joining segment hits
[Mon Jun 14 22:53:28 2010] Reporting output tracks
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Run complete [08:48:38 elapsed]