[Wed Jun 16 10:41:44 2010] Beginning TopHat run (v1.0.13)
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[Wed Jun 16 10:41:44 2010] Preparing output location /projects/NBL/HS1795/700B4AAXX_2/tophat_wj/
[Wed Jun 16 10:41:44 2010] Checking for Bowtie index files
[Wed Jun 16 10:41:44 2010] Checking for reference FASTA file
[Wed Jun 16 10:41:44 2010] Checking for Bowtie
	Bowtie version:		 0.12.5.0
[Wed Jun 16 10:41:45 2010] Checking reads
	seed length:	 75bp
	format:		 fastq
	quality scale:	 phred33 (default)
[Wed Jun 16 10:51:12 2010] Reading known junctions from GFF file
[Wed Jun 16 11:04:53 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 13:03:36 2010] Joining segment hits
	Splitting reads into 3 segments
[Wed Jun 16 13:12:15 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 14:53:44 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 16:40:45 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 18:01:30 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 20:10:06 2010] Joining segment hits
	Splitting reads into 3 segments
[Wed Jun 16 20:43:22 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 22:21:38 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 23:56:49 2010] Mapping reads against hg18 with Bowtie
[Thu Jun 17 01:10:26 2010] Searching for junctions via segment mapping
[Thu Jun 17 01:35:20 2010] Retrieving sequences for splices
[Thu Jun 17 01:40:14 2010] Indexing splices
[Thu Jun 17 02:00:53 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 02:59:18 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 03:57:26 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 04:40:37 2010] Joining segment hits
[Thu Jun 17 05:02:15 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 05:56:57 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 06:51:12 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 07:34:08 2010] Joining segment hits
[Thu Jun 17 08:08:56 2010] Reporting output tracks
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Run complete [01:04:56 elapsed]