[Mon Jun 14 15:37:51 2010] Beginning TopHat run (v1.0.13)
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[Mon Jun 14 15:37:51 2010] Preparing output location /projects/NBL/HS1197/311NGAAXX_4/tophat_wj/
[Mon Jun 14 15:37:51 2010] Checking for Bowtie index files
[Mon Jun 14 15:37:51 2010] Checking for reference FASTA file
[Mon Jun 14 15:37:51 2010] Checking for Bowtie
	Bowtie version:		 0.12.5.0
[Mon Jun 14 15:37:51 2010] Checking reads
	seed length:	 50bp
	format:		 fastq
	quality scale:	 phred33 (default)
[Mon Jun 14 15:42:09 2010] Reading known junctions from GFF file
[Mon Jun 14 16:12:27 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 18:08:38 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 18:16:55 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 18:44:50 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 19:08:41 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 20:51:11 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 20:56:50 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 21:27:45 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 21:57:00 2010] Searching for junctions via segment mapping
[Mon Jun 14 22:16:45 2010] Retrieving sequences for splices
[Mon Jun 14 22:20:02 2010] Indexing splices
[Mon Jun 14 22:34:40 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 22:49:25 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 23:03:26 2010] Joining segment hits
[Mon Jun 14 23:18:00 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 23:34:50 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 23:49:36 2010] Joining segment hits
[Mon Jun 14 23:59:34 2010] Reporting output tracks
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Run complete [10:42:17 elapsed]