[Mon Jun 14 16:15:54 2010] Beginning TopHat run (v1.0.13)
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[Mon Jun 14 16:15:54 2010] Preparing output location /projects/NBL/HS1795/700FNAAXX_8/tophat_wj/
[Mon Jun 14 16:15:54 2010] Checking for Bowtie index files
[Mon Jun 14 16:15:54 2010] Checking for reference FASTA file
[Mon Jun 14 16:15:54 2010] Checking for Bowtie
	Bowtie version:		 0.12.5.0
[Mon Jun 14 16:15:54 2010] Checking reads
	seed length:	 75bp
	format:		 fastq
	quality scale:	 phred33 (default)
[Mon Jun 14 16:21:30 2010] Reading known junctions from GFF file
[Mon Jun 14 16:37:29 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 18:32:38 2010] Joining segment hits
	Splitting reads into 3 segments
[Mon Jun 14 18:42:51 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 19:28:41 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 20:14:27 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 21:00:30 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 22:53:09 2010] Joining segment hits
	Splitting reads into 3 segments
[Mon Jun 14 23:00:14 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 23:50:08 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 00:40:35 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 01:31:15 2010] Searching for junctions via segment mapping
[Tue Jun 15 01:47:31 2010] Retrieving sequences for splices
[Tue Jun 15 01:51:02 2010] Indexing splices
[Tue Jun 15 02:11:41 2010] Mapping reads against segment_juncs with Bowtie
[Tue Jun 15 02:42:42 2010] Mapping reads against segment_juncs with Bowtie
[Tue Jun 15 03:13:46 2010] Mapping reads against segment_juncs with Bowtie
[Tue Jun 15 03:42:51 2010] Joining segment hits
[Tue Jun 15 03:54:00 2010] Mapping reads against segment_juncs with Bowtie
[Tue Jun 15 04:28:11 2010] Mapping reads against segment_juncs with Bowtie
[Tue Jun 15 05:01:27 2010] Mapping reads against segment_juncs with Bowtie
[Tue Jun 15 05:32:44 2010] Joining segment hits
[Tue Jun 15 05:41:47 2010] Reporting output tracks
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Run complete [15:48:20 elapsed]