[Wed Jun 16 10:48:41 2010] Beginning TopHat run (v1.0.13)
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[Wed Jun 16 10:48:41 2010] Preparing output location /projects/NBL/HS1801/61074AAXX_6/tophat_wj/
[Wed Jun 16 10:48:41 2010] Checking for Bowtie index files
[Wed Jun 16 10:48:41 2010] Checking for reference FASTA file
[Wed Jun 16 10:48:41 2010] Checking for Bowtie
	Bowtie version:		 0.12.5.0
[Wed Jun 16 10:48:41 2010] Checking reads
	seed length:	 75bp
	format:		 fastq
	quality scale:	 phred33 (default)
[Wed Jun 16 10:58:08 2010] Reading known junctions from GFF file
[Wed Jun 16 11:12:11 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 13:35:34 2010] Joining segment hits
	Splitting reads into 3 segments
[Wed Jun 16 13:47:13 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 15:22:20 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 16:51:01 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 18:21:19 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 20:56:24 2010] Joining segment hits
	Splitting reads into 3 segments
[Wed Jun 16 21:37:14 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 23:18:02 2010] Mapping reads against hg18 with Bowtie
[Thu Jun 17 00:58:19 2010] Mapping reads against hg18 with Bowtie
[Thu Jun 17 02:37:57 2010] Searching for junctions via segment mapping
[Thu Jun 17 03:03:18 2010] Retrieving sequences for splices
[Thu Jun 17 03:07:09 2010] Indexing splices
[Thu Jun 17 03:29:40 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 04:22:41 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 05:14:52 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 06:05:05 2010] Joining segment hits
[Thu Jun 17 06:30:34 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 07:29:55 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 08:31:49 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 09:29:19 2010] Joining segment hits
[Thu Jun 17 10:37:11 2010] Reporting output tracks
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Run complete [04:49:33 elapsed]