[Mon Jun 14 15:19:39 2010] Beginning TopHat run (v1.0.13)
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[Mon Jun 14 15:19:39 2010] Preparing output location /projects/NBL/HS1198/30UBRAAXX_8/tophat_wj/
[Mon Jun 14 15:19:39 2010] Checking for Bowtie index files
[Mon Jun 14 15:19:39 2010] Checking for reference FASTA file
[Mon Jun 14 15:19:39 2010] Checking for Bowtie
	Bowtie version:		 0.12.5.0
[Mon Jun 14 15:19:39 2010] Checking reads
	seed length:	 50bp
	format:		 fastq
	quality scale:	 phred33 (default)
[Mon Jun 14 15:21:57 2010] Reading known junctions from GFF file
[Mon Jun 14 15:29:27 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 16:31:29 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 16:38:22 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 17:14:04 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 17:46:14 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 18:47:21 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 18:52:43 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 19:33:12 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 20:11:02 2010] Searching for junctions via segment mapping
[Mon Jun 14 20:32:57 2010] Retrieving sequences for splices
[Mon Jun 14 20:35:54 2010] Indexing splices
[Mon Jun 14 20:45:57 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 20:59:51 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 21:12:13 2010] Joining segment hits
[Mon Jun 14 21:19:36 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 21:34:17 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 21:47:19 2010] Joining segment hits
[Mon Jun 14 21:52:14 2010] Reporting output tracks
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Run complete [07:44:12 elapsed]