[Mon Jun 14 14:43:15 2010] Beginning TopHat run (v1.0.13)
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[Mon Jun 14 14:43:15 2010] Preparing output location /projects/NBL/HS1195/30TTYAAXX_7/tophat_wj/
[Mon Jun 14 14:43:15 2010] Checking for Bowtie index files
[Mon Jun 14 14:43:16 2010] Checking for reference FASTA file
[Mon Jun 14 14:43:16 2010] Checking for Bowtie
	Bowtie version:		 0.12.5.0
[Mon Jun 14 14:43:16 2010] Checking reads
	seed length:	 50bp
	format:		 fastq
	quality scale:	 phred33 (default)
[Mon Jun 14 14:45:54 2010] Reading known junctions from GFF file
[Mon Jun 14 14:52:20 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 16:03:21 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 16:10:15 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 16:54:06 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 17:21:14 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 17:44:03 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 17:46:20 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 17:58:20 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 18:57:06 2010] Searching for junctions via segment mapping
[Mon Jun 14 20:17:17 2010] Retrieving sequences for splices
[Mon Jun 14 20:21:21 2010] Indexing splices
[Mon Jun 14 20:44:24 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 21:09:47 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 21:27:33 2010] Joining segment hits
[Mon Jun 14 21:33:56 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 21:47:18 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 22:18:15 2010] Joining segment hits
[Mon Jun 14 22:23:20 2010] Reporting output tracks
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Run complete [08:43:21 elapsed]