[Mon Jun 14 15:20:37 2010] Beginning TopHat run (v1.0.13)
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[Mon Jun 14 15:20:37 2010] Preparing output location /projects/NBL/HS1198/30UBRAAXX_4/tophat_wj/
[Mon Jun 14 15:20:37 2010] Checking for Bowtie index files
[Mon Jun 14 15:20:37 2010] Checking for reference FASTA file
[Mon Jun 14 15:20:37 2010] Checking for Bowtie
	Bowtie version:		 0.12.5.0
[Mon Jun 14 15:20:37 2010] Checking reads
	seed length:	 50bp
	format:		 fastq
	quality scale:	 phred33 (default)
[Mon Jun 14 15:23:09 2010] Reading known junctions from GFF file
[Mon Jun 14 15:32:35 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 16:43:07 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 16:50:54 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 17:32:57 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 18:10:17 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 19:17:26 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 19:21:39 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 20:07:20 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 20:48:45 2010] Searching for junctions via segment mapping
[Mon Jun 14 21:18:09 2010] Retrieving sequences for splices
[Mon Jun 14 21:21:55 2010] Indexing splices
[Mon Jun 14 21:33:21 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 21:50:11 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 22:05:24 2010] Joining segment hits
[Mon Jun 14 22:21:52 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 22:39:15 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 22:55:32 2010] Joining segment hits
[Mon Jun 14 23:05:37 2010] Reporting output tracks
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Run complete [09:01:07 elapsed]