[Mon Jun 14 14:30:23 2010] Beginning TopHat run (v1.0.13)
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[Mon Jun 14 14:30:23 2010] Preparing output location /projects/NBL/HS1194/311L9AAXX_7/tophat_wj/
[Mon Jun 14 14:30:23 2010] Checking for Bowtie index files
[Mon Jun 14 14:30:23 2010] Checking for reference FASTA file
[Mon Jun 14 14:30:23 2010] Checking for Bowtie
	Bowtie version:		 0.12.5.0
[Mon Jun 14 14:30:23 2010] Checking reads
	seed length:	 50bp
	format:		 fastq
	quality scale:	 phred33 (default)
[Mon Jun 14 14:32:49 2010] Reading known junctions from GFF file
[Mon Jun 14 14:37:48 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 15:39:07 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 15:45:28 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 16:29:30 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 17:09:08 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 18:08:21 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 18:13:33 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 19:06:43 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 19:57:11 2010] Searching for junctions via segment mapping
[Mon Jun 14 20:22:21 2010] Retrieving sequences for splices
[Mon Jun 14 20:25:18 2010] Indexing splices
[Mon Jun 14 20:38:20 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 20:53:31 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 21:07:53 2010] Joining segment hits
[Mon Jun 14 21:14:26 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 21:33:40 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 21:51:41 2010] Joining segment hits
[Mon Jun 14 21:57:59 2010] Reporting output tracks
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Run complete [08:38:38 elapsed]