[Wed Jun 16 10:08:04 2010] Beginning TopHat run (v1.0.13)
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[Wed Jun 16 10:08:04 2010] Preparing output location /projects/NBL/HS1194/302P8AAXX_4/tophat_wj/
[Wed Jun 16 10:08:05 2010] Checking for Bowtie index files
[Wed Jun 16 10:08:05 2010] Checking for reference FASTA file
[Wed Jun 16 10:08:05 2010] Checking for Bowtie
	Bowtie version:		 0.12.5.0
[Wed Jun 16 10:08:05 2010] Checking reads
	seed length:	 50bp
	format:		 fastq
	quality scale:	 phred33 (default)
[Wed Jun 16 10:10:26 2010] Reading known junctions from GFF file
[Wed Jun 16 10:15:36 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 11:16:25 2010] Joining segment hits
	Splitting reads into 2 segments
[Wed Jun 16 11:21:38 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 12:05:37 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 12:55:28 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 14:00:45 2010] Joining segment hits
	Splitting reads into 2 segments
[Wed Jun 16 14:04:11 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 14:52:53 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 15:39:29 2010] Searching for junctions via segment mapping
[Wed Jun 16 16:01:12 2010] Retrieving sequences for splices
[Wed Jun 16 16:04:20 2010] Indexing splices
[Wed Jun 16 16:14:31 2010] Mapping reads against segment_juncs with Bowtie
[Wed Jun 16 16:30:16 2010] Mapping reads against segment_juncs with Bowtie
[Wed Jun 16 16:44:47 2010] Joining segment hits
[Wed Jun 16 16:49:57 2010] Mapping reads against segment_juncs with Bowtie
[Wed Jun 16 17:07:12 2010] Mapping reads against segment_juncs with Bowtie
[Wed Jun 16 17:23:43 2010] Joining segment hits
[Wed Jun 16 17:29:15 2010] Reporting output tracks
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Run complete [08:35:57 elapsed]