[Mon Jun 14 14:32:39 2010] Beginning TopHat run (v1.0.13)
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[Mon Jun 14 14:32:39 2010] Preparing output location /projects/NBL/HS1194/302P8AAXX_4/tophat_wj/
[Mon Jun 14 14:32:39 2010] Checking for Bowtie index files
[Mon Jun 14 14:32:39 2010] Checking for reference FASTA file
[Mon Jun 14 14:32:39 2010] Checking for Bowtie
	Bowtie version:		 0.12.5.0
[Mon Jun 14 14:32:40 2010] Checking reads
	seed length:	 50bp
	format:		 fastq
	quality scale:	 phred33 (default)
[Mon Jun 14 14:35:42 2010] Reading known junctions from GFF file
[Mon Jun 14 14:42:19 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 16:04:37 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 16:14:46 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 17:13:54 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 18:09:34 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 19:19:40 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 19:23:42 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 20:20:44 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 21:14:37 2010] Searching for junctions via segment mapping
[Mon Jun 14 21:40:33 2010] Retrieving sequences for splices
[Mon Jun 14 21:44:11 2010] Indexing splices
[Mon Jun 14 21:57:24 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 22:16:23 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 22:34:00 2010] Joining segment hits
[Mon Jun 14 22:40:17 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 23:00:26 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 23:19:57 2010] Joining segment hits
[Mon Jun 14 23:24:16 2010] Reporting output tracks
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Run complete [09:09:49 elapsed]