[Mon Jun 14 14:23:01 2010] Beginning TopHat run (v1.0.13)
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[Mon Jun 14 14:23:01 2010] Preparing output location /projects/NBL/HS1194/311L9AAXX_4/tophat_wj/
[Mon Jun 14 14:23:01 2010] Checking for Bowtie index files
[Mon Jun 14 14:23:01 2010] Checking for reference FASTA file
[Mon Jun 14 14:23:01 2010] Checking for Bowtie
	Bowtie version:		 0.12.5.0
[Mon Jun 14 14:23:01 2010] Checking reads
	seed length:	 50bp
	format:		 fastq
	quality scale:	 phred33 (default)
[Mon Jun 14 14:25:23 2010] Reading known junctions from GFF file
[Mon Jun 14 14:30:33 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 15:45:10 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 16:02:51 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 16:50:50 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 17:30:05 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 18:31:10 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 18:41:04 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 19:37:09 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 20:28:32 2010] Searching for junctions via segment mapping
[Mon Jun 14 20:53:58 2010] Retrieving sequences for splices
[Mon Jun 14 20:56:54 2010] Indexing splices
[Mon Jun 14 21:08:01 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 21:23:34 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 21:38:16 2010] Joining segment hits
[Mon Jun 14 21:43:22 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 22:02:31 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 22:20:12 2010] Joining segment hits
[Mon Jun 14 22:26:26 2010] Reporting output tracks
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Run complete [09:10:15 elapsed]