[Mon Jun 14 15:23:11 2010] Beginning TopHat run (v1.0.13)
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[Mon Jun 14 15:23:11 2010] Preparing output location /projects/NBL/HS1197/311NGAAXX_7/tophat_wj/
[Mon Jun 14 15:23:11 2010] Checking for Bowtie index files
[Mon Jun 14 15:23:11 2010] Checking for reference FASTA file
[Mon Jun 14 15:23:11 2010] Checking for Bowtie
	Bowtie version:		 0.12.5.0
[Mon Jun 14 15:23:11 2010] Checking reads
	seed length:	 50bp
	format:		 fastq
	quality scale:	 phred33 (default)
[Mon Jun 14 15:26:59 2010] Reading known junctions from GFF file
[Mon Jun 14 15:36:05 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 17:19:44 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 17:26:26 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 17:50:27 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 18:13:29 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 19:55:13 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 20:00:09 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 20:31:00 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 21:00:39 2010] Searching for junctions via segment mapping
[Mon Jun 14 21:19:10 2010] Retrieving sequences for splices
[Mon Jun 14 21:22:17 2010] Indexing splices
[Mon Jun 14 21:37:08 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 21:52:18 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 22:06:03 2010] Joining segment hits
[Mon Jun 14 22:17:16 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 22:34:37 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 22:49:48 2010] Joining segment hits
[Mon Jun 14 23:01:31 2010] Reporting output tracks
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Run complete [09:53:07 elapsed]