[Mon Jun 14 16:08:32 2010] Beginning TopHat run (v1.0.13)
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[Mon Jun 14 16:08:32 2010] Preparing output location /projects/NBL/HS1197/311NGAAXX_6/tophat_wj/
[Mon Jun 14 16:08:33 2010] Checking for Bowtie index files
[Mon Jun 14 16:08:33 2010] Checking for reference FASTA file
[Mon Jun 14 16:08:33 2010] Checking for Bowtie
	Bowtie version:		 0.12.5.0
[Mon Jun 14 16:08:33 2010] Checking reads
	seed length:	 50bp
	format:		 fastq
	quality scale:	 phred33 (default)
[Mon Jun 14 16:15:16 2010] Reading known junctions from GFF file
[Mon Jun 14 16:29:26 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 18:40:26 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 18:54:59 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 19:26:17 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 19:54:24 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 21:48:04 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 21:53:35 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 22:30:56 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 23:05:29 2010] Searching for junctions via segment mapping
[Mon Jun 14 23:30:21 2010] Retrieving sequences for splices
[Mon Jun 14 23:34:48 2010] Indexing splices
[Mon Jun 14 23:55:50 2010] Mapping reads against segment_juncs with Bowtie
[Tue Jun 15 00:20:14 2010] Mapping reads against segment_juncs with Bowtie
[Tue Jun 15 00:43:09 2010] Joining segment hits
[Tue Jun 15 00:51:13 2010] Mapping reads against segment_juncs with Bowtie
[Tue Jun 15 01:18:56 2010] Mapping reads against segment_juncs with Bowtie
[Tue Jun 15 01:43:32 2010] Joining segment hits
[Tue Jun 15 01:52:15 2010] Reporting output tracks
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Run complete [10:21:10 elapsed]