[Mon Jun 14 15:52:52 2010] Beginning TopHat run (v1.0.13)
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[Mon Jun 14 15:52:52 2010] Preparing output location /projects/NBL/HS1197/311NGAAXX_3/tophat_wj/
[Mon Jun 14 15:52:53 2010] Checking for Bowtie index files
[Mon Jun 14 15:52:53 2010] Checking for reference FASTA file
[Mon Jun 14 15:52:53 2010] Checking for Bowtie
	Bowtie version:		 0.12.5.0
[Mon Jun 14 15:52:53 2010] Checking reads
	seed length:	 50bp
	format:		 fastq
	quality scale:	 phred33 (default)
[Mon Jun 14 15:59:04 2010] Reading known junctions from GFF file
[Mon Jun 14 16:15:41 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 18:35:25 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 18:51:08 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 19:29:21 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 19:58:13 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 21:59:57 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 22:06:48 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 22:47:56 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 23:28:21 2010] Searching for junctions via segment mapping
[Mon Jun 14 23:50:52 2010] Retrieving sequences for splices
[Mon Jun 14 23:54:44 2010] Indexing splices
[Tue Jun 15 00:14:29 2010] Mapping reads against segment_juncs with Bowtie
[Tue Jun 15 00:33:11 2010] Mapping reads against segment_juncs with Bowtie
[Tue Jun 15 00:48:47 2010] Joining segment hits
[Tue Jun 15 00:56:57 2010] Mapping reads against segment_juncs with Bowtie
[Tue Jun 15 01:16:51 2010] Mapping reads against segment_juncs with Bowtie
[Tue Jun 15 01:35:12 2010] Joining segment hits
[Tue Jun 15 01:42:34 2010] Reporting output tracks
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Run complete [10:22:11 elapsed]