[Wed Jun 16 10:53:40 2010] Beginning TopHat run (v1.0.13)
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[Wed Jun 16 10:53:40 2010] Preparing output location /projects/NBL/HS1801/61074AAXX_8/tophat_wj/
[Wed Jun 16 10:53:40 2010] Checking for Bowtie index files
[Wed Jun 16 10:53:40 2010] Checking for reference FASTA file
[Wed Jun 16 10:53:40 2010] Checking for Bowtie
	Bowtie version:		 0.12.5.0
[Wed Jun 16 10:53:40 2010] Checking reads
	seed length:	 75bp
	format:		 fastq
	quality scale:	 phred33 (default)
[Wed Jun 16 11:02:20 2010] Reading known junctions from GFF file
[Wed Jun 16 11:17:57 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 13:51:43 2010] Joining segment hits
	Splitting reads into 3 segments
[Wed Jun 16 14:01:10 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 15:38:14 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 17:09:37 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 18:42:24 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 21:10:33 2010] Joining segment hits
	Splitting reads into 3 segments
[Wed Jun 16 21:43:46 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 23:26:30 2010] Mapping reads against hg18 with Bowtie
[Thu Jun 17 01:07:51 2010] Mapping reads against hg18 with Bowtie
[Thu Jun 17 02:48:00 2010] Searching for junctions via segment mapping
[Thu Jun 17 03:12:51 2010] Retrieving sequences for splices
[Thu Jun 17 03:16:42 2010] Indexing splices
[Thu Jun 17 03:39:03 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 04:33:33 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 05:27:32 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 06:19:00 2010] Joining segment hits
[Thu Jun 17 06:43:30 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 07:43:03 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 08:43:39 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 09:41:48 2010] Joining segment hits
[Thu Jun 17 10:42:32 2010] Reporting output tracks
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Run complete [03:48:00 elapsed]