[Wed Jun 16 10:49:18 2010] Beginning TopHat run (v1.0.13)
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[Wed Jun 16 10:49:18 2010] Preparing output location /projects/NBL/HS1799/61074AAXX_5/tophat_wj/
[Wed Jun 16 10:49:18 2010] Checking for Bowtie index files
[Wed Jun 16 10:49:18 2010] Checking for reference FASTA file
[Wed Jun 16 10:49:18 2010] Checking for Bowtie
	Bowtie version:		 0.12.5.0
[Wed Jun 16 10:49:18 2010] Checking reads
	seed length:	 75bp
	format:		 fastq
	quality scale:	 phred33 (default)
[Wed Jun 16 10:58:11 2010] Reading known junctions from GFF file
[Wed Jun 16 11:12:59 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 13:32:33 2010] Joining segment hits
	Splitting reads into 3 segments
[Wed Jun 16 13:42:25 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 15:09:10 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 16:40:58 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 18:10:26 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 20:58:09 2010] Joining segment hits
	Splitting reads into 3 segments
[Wed Jun 16 21:48:16 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 23:20:41 2010] Mapping reads against hg18 with Bowtie
[Thu Jun 17 00:50:57 2010] Mapping reads against hg18 with Bowtie
[Thu Jun 17 02:20:58 2010] Searching for junctions via segment mapping
[Thu Jun 17 02:40:52 2010] Retrieving sequences for splices
[Thu Jun 17 02:44:52 2010] Indexing splices
[Thu Jun 17 03:07:23 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 03:56:34 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 04:48:28 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 05:34:28 2010] Joining segment hits
[Thu Jun 17 05:58:10 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 06:49:25 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 07:42:00 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 08:31:13 2010] Joining segment hits
[Thu Jun 17 09:33:39 2010] Reporting output tracks
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Run complete [03:26:34 elapsed]