[Mon Jun 14 14:29:32 2010] Beginning TopHat run (v1.0.13)
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[Mon Jun 14 14:29:32 2010] Preparing output location /projects/NBL/HS1194/311L9AAXX_5/tophat_wj/
[Mon Jun 14 14:29:32 2010] Checking for Bowtie index files
[Mon Jun 14 14:29:32 2010] Checking for reference FASTA file
[Mon Jun 14 14:29:32 2010] Checking for Bowtie
	Bowtie version:		 0.12.5.0
[Mon Jun 14 14:29:32 2010] Checking reads
	seed length:	 50bp
	format:		 fastq
	quality scale:	 phred33 (default)
[Mon Jun 14 14:32:02 2010] Reading known junctions from GFF file
[Mon Jun 14 14:37:01 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 16:05:55 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 16:17:36 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 16:59:45 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 17:37:39 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 18:35:50 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 18:43:26 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 19:33:33 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 20:21:27 2010] Searching for junctions via segment mapping
[Mon Jun 14 20:45:48 2010] Retrieving sequences for splices
[Mon Jun 14 20:48:40 2010] Indexing splices
[Mon Jun 14 20:59:29 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 21:14:18 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 21:28:21 2010] Joining segment hits
[Mon Jun 14 21:34:24 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 21:52:21 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 22:09:07 2010] Joining segment hits
[Mon Jun 14 22:17:34 2010] Reporting output tracks
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Run complete [08:54:50 elapsed]