[Mon Jun 14 14:50:01 2010] Beginning TopHat run (v1.0.13)
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[Mon Jun 14 14:50:01 2010] Preparing output location /projects/NBL/HS1196/3153YAAXX_4/tophat_wj/
[Mon Jun 14 14:50:01 2010] Checking for Bowtie index files
[Mon Jun 14 14:50:01 2010] Checking for reference FASTA file
[Mon Jun 14 14:50:01 2010] Checking for Bowtie
	Bowtie version:		 0.12.5.0
[Mon Jun 14 14:50:01 2010] Checking reads
	seed length:	 50bp
	format:		 fastq
	quality scale:	 phred33 (default)
[Mon Jun 14 14:52:18 2010] Reading known junctions from GFF file
[Mon Jun 14 14:57:06 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 16:01:11 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 16:08:32 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 16:38:18 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 17:06:22 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 18:02:54 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 18:06:38 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 18:45:44 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 19:19:47 2010] Searching for junctions via segment mapping
[Mon Jun 14 19:38:27 2010] Retrieving sequences for splices
[Mon Jun 14 19:41:22 2010] Indexing splices
[Mon Jun 14 19:51:30 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 20:03:48 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 20:14:53 2010] Joining segment hits
[Mon Jun 14 20:21:13 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 20:35:34 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 20:49:02 2010] Joining segment hits
[Mon Jun 14 20:53:47 2010] Reporting output tracks
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Run complete [07:21:05 elapsed]