[Mon Jun 14 14:20:12 2010] Beginning TopHat run (v1.0.13)
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[Mon Jun 14 14:20:12 2010] Preparing output location /projects/NBL/HS1194/311L9AAXX_3/tophat_wj/
[Mon Jun 14 14:20:12 2010] Checking for Bowtie index files
[Mon Jun 14 14:20:12 2010] Checking for reference FASTA file
[Mon Jun 14 14:20:12 2010] Checking for Bowtie
	Bowtie version:		 0.12.5.0
[Mon Jun 14 14:20:12 2010] Checking reads
	seed length:	 50bp
	format:		 fastq
	quality scale:	 phred33 (default)
[Mon Jun 14 14:22:38 2010] Reading known junctions from GFF file
[Mon Jun 14 14:27:33 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 15:30:44 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 15:36:17 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 16:19:50 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 16:58:59 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 17:57:09 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 18:01:09 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 18:53:07 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 19:43:33 2010] Searching for junctions via segment mapping
[Mon Jun 14 20:07:56 2010] Retrieving sequences for splices
[Mon Jun 14 20:10:50 2010] Indexing splices
[Mon Jun 14 20:20:55 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 20:36:08 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 20:50:27 2010] Joining segment hits
[Mon Jun 14 20:56:39 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 21:14:52 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 21:31:45 2010] Joining segment hits
[Mon Jun 14 21:35:59 2010] Reporting output tracks
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Run complete [08:24:14 elapsed]