[Mon Jun 14 15:03:17 2010] Beginning TopHat run (v1.0.13)
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[Mon Jun 14 15:03:17 2010] Preparing output location /projects/NBL/HS1196/3153YAAXX_8/tophat_wj/
[Mon Jun 14 15:03:17 2010] Checking for Bowtie index files
[Mon Jun 14 15:03:17 2010] Checking for reference FASTA file
[Mon Jun 14 15:03:17 2010] Checking for Bowtie
	Bowtie version:		 0.12.5.0
[Mon Jun 14 15:03:17 2010] Checking reads
	seed length:	 50bp
	format:		 fastq
	quality scale:	 phred33 (default)
[Mon Jun 14 15:05:41 2010] Reading known junctions from GFF file
[Mon Jun 14 15:13:36 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 16:15:55 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 16:23:33 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 16:52:14 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 17:19:15 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 18:18:19 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 18:26:11 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 18:57:52 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 19:29:10 2010] Searching for junctions via segment mapping
[Mon Jun 14 19:46:25 2010] Retrieving sequences for splices
[Mon Jun 14 19:49:21 2010] Indexing splices
[Mon Jun 14 19:59:06 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 20:11:10 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 20:22:13 2010] Joining segment hits
[Mon Jun 14 20:29:00 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 20:42:44 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 20:55:15 2010] Joining segment hits
[Mon Jun 14 20:59:03 2010] Reporting output tracks
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Run complete [07:13:39 elapsed]