[Mon Jun 14 14:32:32 2010] Beginning TopHat run (v1.0.13)
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[Mon Jun 14 14:32:32 2010] Preparing output location /projects/NBL/HS1195/302NNAAXX_5/tophat_wj/
[Mon Jun 14 14:32:32 2010] Checking for Bowtie index files
[Mon Jun 14 14:32:32 2010] Checking for reference FASTA file
[Mon Jun 14 14:32:32 2010] Checking for Bowtie
	Bowtie version:		 0.12.5.0
[Mon Jun 14 14:32:32 2010] Checking reads
	seed length:	 50bp
	format:		 fastq
	quality scale:	 phred33 (default)
[Mon Jun 14 14:34:50 2010] Reading known junctions from GFF file
[Mon Jun 14 14:40:35 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 15:33:05 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 15:39:26 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 16:20:04 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 16:46:35 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 17:34:32 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 17:39:04 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 18:22:23 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 19:07:22 2010] Searching for junctions via segment mapping
[Mon Jun 14 20:07:31 2010] Retrieving sequences for splices
[Mon Jun 14 20:12:24 2010] Indexing splices
[Mon Jun 14 20:33:13 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 20:56:41 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 21:13:05 2010] Joining segment hits
[Mon Jun 14 21:17:19 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 21:42:17 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 22:06:15 2010] Joining segment hits
[Mon Jun 14 22:11:50 2010] Reporting output tracks
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Run complete [08:39:36 elapsed]