[Wed Jun 16 11:10:51 2010] Beginning TopHat run (v1.0.13)
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[Wed Jun 16 11:10:51 2010] Preparing output location /projects/NBL/HS1797/616GYAAXX_2/tophat_wj/
[Wed Jun 16 11:10:51 2010] Checking for Bowtie index files
[Wed Jun 16 11:10:51 2010] Checking for reference FASTA file
[Wed Jun 16 11:10:51 2010] Checking for Bowtie
	Bowtie version:		 0.12.5.0
[Wed Jun 16 11:10:51 2010] Checking reads
	seed length:	 75bp
	format:		 fastq
	quality scale:	 phred33 (default)
[Wed Jun 16 11:21:11 2010] Reading known junctions from GFF file
[Wed Jun 16 11:36:41 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 14:35:18 2010] Joining segment hits
	Splitting reads into 3 segments
[Wed Jun 16 14:44:37 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 16:36:34 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 18:23:16 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 20:22:53 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 23:43:42 2010] Joining segment hits
	Splitting reads into 3 segments
[Thu Jun 17 00:19:08 2010] Mapping reads against hg18 with Bowtie
[Thu Jun 17 02:07:11 2010] Mapping reads against hg18 with Bowtie
[Thu Jun 17 03:55:39 2010] Mapping reads against hg18 with Bowtie
[Thu Jun 17 05:29:51 2010] Searching for junctions via segment mapping
[Thu Jun 17 05:52:44 2010] Retrieving sequences for splices
[Thu Jun 17 05:57:44 2010] Indexing splices
[Thu Jun 17 06:28:29 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 07:35:57 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 08:41:31 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 09:41:59 2010] Joining segment hits
[Thu Jun 17 11:10:40 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 12:14:24 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 13:14:58 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 14:22:02 2010] Joining segment hits
[Thu Jun 17 16:39:25 2010] Reporting output tracks
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Run complete [07:13:19 elapsed]