[Wed Jun 16 11:33:58 2010] Beginning TopHat run (v1.0.13)
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[Wed Jun 16 11:33:58 2010] Preparing output location /projects/NBL/HS1795/700B4AAXX_3/tophat_wj/
[Wed Jun 16 11:33:58 2010] Checking for Bowtie index files
[Wed Jun 16 11:33:58 2010] Checking for reference FASTA file
[Wed Jun 16 11:33:58 2010] Checking for Bowtie
	Bowtie version:		 0.12.5.0
[Wed Jun 16 11:33:58 2010] Checking reads
	seed length:	 75bp
	format:		 fastq
	quality scale:	 phred33 (default)
[Wed Jun 16 11:45:29 2010] Reading known junctions from GFF file
[Wed Jun 16 12:12:48 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 15:05:40 2010] Joining segment hits
	Splitting reads into 3 segments
[Wed Jun 16 15:24:08 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 17:11:31 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 18:54:54 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 20:43:50 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 23:37:18 2010] Joining segment hits
	Splitting reads into 3 segments
[Thu Jun 17 00:04:19 2010] Mapping reads against hg18 with Bowtie
[Thu Jun 17 01:57:25 2010] Mapping reads against hg18 with Bowtie
[Thu Jun 17 03:50:25 2010] Mapping reads against hg18 with Bowtie
[Thu Jun 17 05:28:23 2010] Searching for junctions via segment mapping
[Thu Jun 17 06:00:44 2010] Retrieving sequences for splices
[Thu Jun 17 06:08:20 2010] Indexing splices
[Thu Jun 17 06:43:56 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 07:57:15 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 09:08:55 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 10:17:22 2010] Joining segment hits
[Thu Jun 17 11:37:39 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 12:54:13 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 14:07:47 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 15:23:35 2010] Joining segment hits
[Thu Jun 17 16:32:36 2010] Reporting output tracks
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Run complete [07:39:56 elapsed]