[Mon Jun 14 14:30:52 2010] Beginning TopHat run (v1.0.13)
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[Mon Jun 14 14:30:52 2010] Preparing output location /projects/NBL/HS1194/311L9AAXX_6/tophat_wj/
[Mon Jun 14 14:30:52 2010] Checking for Bowtie index files
[Mon Jun 14 14:30:52 2010] Checking for reference FASTA file
[Mon Jun 14 14:30:52 2010] Checking for Bowtie
	Bowtie version:		 0.12.5.0
[Mon Jun 14 14:30:52 2010] Checking reads
	seed length:	 50bp
	format:		 fastq
	quality scale:	 phred33 (default)
[Mon Jun 14 14:33:21 2010] Reading known junctions from GFF file
[Mon Jun 14 14:38:23 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 15:44:06 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 15:54:59 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 16:41:00 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 17:20:20 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 18:22:29 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 18:27:18 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 19:20:42 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 20:08:50 2010] Searching for junctions via segment mapping
[Mon Jun 14 20:34:00 2010] Retrieving sequences for splices
[Mon Jun 14 20:37:27 2010] Indexing splices
[Mon Jun 14 20:47:43 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 21:03:19 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 21:17:29 2010] Joining segment hits
[Mon Jun 14 21:23:29 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 21:41:30 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 21:58:14 2010] Joining segment hits
[Mon Jun 14 22:05:59 2010] Reporting output tracks
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Run complete [08:46:14 elapsed]