[Mon Jun 14 15:09:17 2010] Beginning TopHat run (v1.0.13)
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[Mon Jun 14 15:09:17 2010] Preparing output location /projects/NBL/HS1198/302P8AAXX_5/tophat_wj/
[Mon Jun 14 15:09:17 2010] Checking for Bowtie index files
[Mon Jun 14 15:09:17 2010] Checking for reference FASTA file
[Mon Jun 14 15:09:17 2010] Checking for Bowtie
	Bowtie version:		 0.12.5.0
[Mon Jun 14 15:09:17 2010] Checking reads
	seed length:	 50bp
	format:		 fastq
	quality scale:	 phred33 (default)
[Mon Jun 14 15:11:50 2010] Reading known junctions from GFF file
[Mon Jun 14 15:20:59 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 17:06:16 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 17:16:34 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 17:55:43 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 18:32:35 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 19:41:59 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 19:45:52 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 20:30:02 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 21:12:44 2010] Searching for junctions via segment mapping
[Mon Jun 14 21:38:00 2010] Retrieving sequences for splices
[Mon Jun 14 21:40:56 2010] Indexing splices
[Mon Jun 14 21:51:15 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 22:06:19 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 22:20:18 2010] Joining segment hits
[Mon Jun 14 22:29:59 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 22:47:15 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 23:03:22 2010] Joining segment hits
[Mon Jun 14 23:13:45 2010] Reporting output tracks
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Run complete [09:23:39 elapsed]