[Wed Jun 16 10:59:04 2010] Beginning TopHat run (v1.0.13)
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[Wed Jun 16 10:59:04 2010] Preparing output location /projects/NBL/HS1799/61B1HAAXX_7/tophat_wj/
[Wed Jun 16 10:59:04 2010] Checking for Bowtie index files
[Wed Jun 16 10:59:04 2010] Checking for reference FASTA file
[Wed Jun 16 10:59:04 2010] Checking for Bowtie
	Bowtie version:		 0.12.5.0
[Wed Jun 16 10:59:04 2010] Checking reads
	seed length:	 75bp
	format:		 fastq
	quality scale:	 phred33 (default)
[Wed Jun 16 11:07:36 2010] Reading known junctions from GFF file
[Wed Jun 16 11:24:27 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 13:42:51 2010] Joining segment hits
	Splitting reads into 3 segments
[Wed Jun 16 13:52:32 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 15:16:39 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 16:41:03 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 18:05:03 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 20:43:09 2010] Joining segment hits
	Splitting reads into 3 segments
[Wed Jun 16 21:34:23 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 22:54:21 2010] Mapping reads against hg18 with Bowtie
[Thu Jun 17 00:13:18 2010] Mapping reads against hg18 with Bowtie
[Thu Jun 17 01:31:54 2010] Searching for junctions via segment mapping
[Thu Jun 17 01:50:24 2010] Retrieving sequences for splices
[Thu Jun 17 01:54:31 2010] Indexing splices
[Thu Jun 17 02:17:02 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 03:05:57 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 03:53:12 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 04:37:54 2010] Joining segment hits
[Thu Jun 17 05:07:02 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 05:53:35 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 06:39:03 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 07:22:43 2010] Joining segment hits
[Thu Jun 17 08:19:20 2010] Reporting output tracks
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Run complete [03:23:49 elapsed]