[Wed Jun 16 11:33:09 2010] Beginning TopHat run (v1.0.13)
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[Wed Jun 16 11:33:09 2010] Preparing output location /projects/NBL/HS1799/61074AAXX_4/tophat_wj/
[Wed Jun 16 11:33:09 2010] Checking for Bowtie index files
[Wed Jun 16 11:33:09 2010] Checking for reference FASTA file
[Wed Jun 16 11:33:09 2010] Checking for Bowtie
	Bowtie version:		 0.12.5.0
[Wed Jun 16 11:33:10 2010] Checking reads
	seed length:	 75bp
	format:		 fastq
	quality scale:	 phred33 (default)
[Wed Jun 16 11:44:30 2010] Reading known junctions from GFF file
[Wed Jun 16 12:10:40 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 15:02:36 2010] Joining segment hits
	Splitting reads into 3 segments
[Wed Jun 16 15:21:00 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 17:01:29 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 18:31:30 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 20:09:28 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 22:51:50 2010] Joining segment hits
	Splitting reads into 3 segments
[Wed Jun 16 23:21:08 2010] Mapping reads against hg18 with Bowtie
[Thu Jun 17 01:05:58 2010] Mapping reads against hg18 with Bowtie
[Thu Jun 17 02:42:56 2010] Mapping reads against hg18 with Bowtie
[Thu Jun 17 04:18:09 2010] Searching for junctions via segment mapping
[Thu Jun 17 04:47:09 2010] Retrieving sequences for splices
[Thu Jun 17 04:54:49 2010] Indexing splices
[Thu Jun 17 05:29:19 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 06:36:56 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 07:41:33 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 08:45:44 2010] Joining segment hits
[Thu Jun 17 09:53:37 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 11:10:09 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 12:20:10 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 13:29:36 2010] Joining segment hits
[Thu Jun 17 14:35:43 2010] Reporting output tracks
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Run complete [06:20:45 elapsed]