[Wed Jun 16 11:33:10 2010] Beginning TopHat run (v1.0.13)
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[Wed Jun 16 11:33:10 2010] Preparing output location /projects/NBL/HS1795/700B4AAXX_4/tophat_wj/
[Wed Jun 16 11:33:10 2010] Checking for Bowtie index files
[Wed Jun 16 11:33:10 2010] Checking for reference FASTA file
[Wed Jun 16 11:33:10 2010] Checking for Bowtie
	Bowtie version:		 0.12.5.0
[Wed Jun 16 11:33:11 2010] Checking reads
	seed length:	 75bp
	format:		 fastq
	quality scale:	 phred33 (default)
[Wed Jun 16 11:44:39 2010] Reading known junctions from GFF file
[Wed Jun 16 12:10:58 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 15:02:50 2010] Joining segment hits
	Splitting reads into 3 segments
[Wed Jun 16 15:21:13 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 17:07:16 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 18:44:35 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 20:25:44 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 23:04:58 2010] Joining segment hits
	Splitting reads into 3 segments
[Wed Jun 16 23:33:23 2010] Mapping reads against hg18 with Bowtie
[Thu Jun 17 01:22:07 2010] Mapping reads against hg18 with Bowtie
[Thu Jun 17 03:00:38 2010] Mapping reads against hg18 with Bowtie
[Thu Jun 17 04:46:56 2010] Searching for junctions via segment mapping
[Thu Jun 17 05:18:21 2010] Retrieving sequences for splices
[Thu Jun 17 05:26:15 2010] Indexing splices
[Thu Jun 17 06:00:31 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 07:18:51 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 08:34:38 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 09:41:43 2010] Joining segment hits
[Thu Jun 17 10:56:51 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 12:12:24 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 13:30:04 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 14:44:56 2010] Joining segment hits
[Thu Jun 17 15:48:53 2010] Reporting output tracks
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Run complete [07:11:01 elapsed]