[Wed Jun 16 10:53:14 2010] Beginning TopHat run (v1.0.13)
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[Wed Jun 16 10:53:14 2010] Preparing output location /projects/NBL/HS1801/61074AAXX_7/tophat_wj/
[Wed Jun 16 10:53:14 2010] Checking for Bowtie index files
[Wed Jun 16 10:53:14 2010] Checking for reference FASTA file
[Wed Jun 16 10:53:14 2010] Checking for Bowtie
	Bowtie version:		 0.12.5.0
[Wed Jun 16 10:53:14 2010] Checking reads
	seed length:	 75bp
	format:		 fastq
	quality scale:	 phred33 (default)
[Wed Jun 16 11:01:45 2010] Reading known junctions from GFF file
[Wed Jun 16 11:17:41 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 13:38:13 2010] Joining segment hits
	Splitting reads into 3 segments
[Wed Jun 16 13:49:45 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 15:23:11 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 16:52:40 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 18:22:11 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 21:12:58 2010] Joining segment hits
	Splitting reads into 3 segments
[Wed Jun 16 21:55:57 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 23:41:53 2010] Mapping reads against hg18 with Bowtie
[Thu Jun 17 01:28:29 2010] Mapping reads against hg18 with Bowtie
[Thu Jun 17 03:12:11 2010] Searching for junctions via segment mapping
[Thu Jun 17 03:37:42 2010] Retrieving sequences for splices
[Thu Jun 17 03:42:11 2010] Indexing splices
[Thu Jun 17 04:06:07 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 05:00:37 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 05:53:41 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 06:44:09 2010] Joining segment hits
[Thu Jun 17 07:15:37 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 08:14:37 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 09:13:41 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 10:10:14 2010] Joining segment hits
[Thu Jun 17 11:25:13 2010] Reporting output tracks
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Run complete [04:59:47 elapsed]