[Wed Jun 16 10:49:34 2010] Beginning TopHat run (v1.0.13)
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[Wed Jun 16 10:49:34 2010] Preparing output location /projects/NBL/HS1803/616GYAAXX_4/tophat_wj/
[Wed Jun 16 10:49:34 2010] Checking for Bowtie index files
[Wed Jun 16 10:49:34 2010] Checking for reference FASTA file
[Wed Jun 16 10:49:34 2010] Checking for Bowtie
	Bowtie version:		 0.12.5.0
[Wed Jun 16 10:49:37 2010] Checking reads
	seed length:	 75bp
	format:		 fastq
	quality scale:	 phred33 (default)
[Wed Jun 16 10:58:00 2010] Reading known junctions from GFF file
[Wed Jun 16 11:11:58 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 13:38:09 2010] Joining segment hits
	Splitting reads into 3 segments
[Wed Jun 16 13:48:24 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 15:16:34 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 16:46:34 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 18:08:27 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 20:51:50 2010] Joining segment hits
	Splitting reads into 3 segments
[Wed Jun 16 21:42:31 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 23:10:14 2010] Mapping reads against hg18 with Bowtie
[Thu Jun 17 00:40:34 2010] Mapping reads against hg18 with Bowtie
[Thu Jun 17 02:07:41 2010] Searching for junctions via segment mapping
[Thu Jun 17 02:28:46 2010] Retrieving sequences for splices
[Thu Jun 17 02:33:10 2010] Indexing splices
[Thu Jun 17 02:56:55 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 03:46:10 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 04:34:36 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 05:19:18 2010] Joining segment hits
[Thu Jun 17 05:42:37 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 06:32:35 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 07:23:08 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 08:09:57 2010] Joining segment hits
[Thu Jun 17 08:53:51 2010] Reporting output tracks
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Run complete [02:36:00 elapsed]