[Mon Jun 14 16:42:11 2010] Beginning TopHat run (v1.0.13)
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[Mon Jun 14 16:42:11 2010] Preparing output location /projects/NBL/HS1797/616GYAAXX_3/tophat_wj/
[Mon Jun 14 16:42:11 2010] Checking for Bowtie index files
[Mon Jun 14 16:42:11 2010] Checking for reference FASTA file
[Mon Jun 14 16:42:11 2010] Checking for Bowtie
	Bowtie version:		 0.12.5.0
[Mon Jun 14 16:42:12 2010] Checking reads
	seed length:	 75bp
	format:		 fastq
	quality scale:	 phred33 (default)
[Mon Jun 14 16:49:47 2010] Reading known junctions from GFF file
[Mon Jun 14 17:13:52 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 19:27:38 2010] Joining segment hits
	Splitting reads into 3 segments
[Mon Jun 14 19:35:27 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 21:00:35 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 22:21:46 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 23:41:32 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 01:43:29 2010] Joining segment hits
	Splitting reads into 3 segments
[Tue Jun 15 01:50:56 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 03:10:20 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 04:30:56 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 05:44:59 2010] Searching for junctions via segment mapping
[Tue Jun 15 06:03:38 2010] Retrieving sequences for splices
[Tue Jun 15 06:07:06 2010] Indexing splices
[Tue Jun 15 06:29:33 2010] Mapping reads against segment_juncs with Bowtie
[Tue Jun 15 07:17:59 2010] Mapping reads against segment_juncs with Bowtie
[Tue Jun 15 08:05:28 2010] Mapping reads against segment_juncs with Bowtie
[Tue Jun 15 08:50:21 2010] Joining segment hits
[Tue Jun 15 09:00:22 2010] Mapping reads against segment_juncs with Bowtie
[Tue Jun 15 09:49:09 2010] Mapping reads against segment_juncs with Bowtie
[Tue Jun 15 10:39:08 2010] Mapping reads against segment_juncs with Bowtie
[Tue Jun 15 11:23:39 2010] Joining segment hits
[Tue Jun 15 11:40:06 2010] Reporting output tracks
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Run complete [21:54:49 elapsed]