[Wed Jun 16 10:37:41 2010] Beginning TopHat run (v1.0.13)
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[Wed Jun 16 10:37:41 2010] Preparing output location /projects/NBL/HS1801/61B1HAAXX_8/tophat_wj/
[Wed Jun 16 10:37:41 2010] Checking for Bowtie index files
[Wed Jun 16 10:37:41 2010] Checking for reference FASTA file
[Wed Jun 16 10:37:41 2010] Checking for Bowtie
	Bowtie version:		 0.12.5.0
[Wed Jun 16 10:37:41 2010] Checking reads
	seed length:	 75bp
	format:		 fastq
	quality scale:	 phred33 (default)
[Wed Jun 16 10:45:14 2010] Reading known junctions from GFF file
[Wed Jun 16 10:58:05 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 12:54:27 2010] Joining segment hits
	Splitting reads into 3 segments
[Wed Jun 16 13:03:09 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 14:18:23 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 15:34:03 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 16:48:48 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 18:49:14 2010] Joining segment hits
	Splitting reads into 3 segments
[Wed Jun 16 19:15:03 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 20:37:18 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 22:00:54 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 23:23:36 2010] Searching for junctions via segment mapping
[Wed Jun 16 23:46:00 2010] Retrieving sequences for splices
[Wed Jun 16 23:51:23 2010] Indexing splices
[Thu Jun 17 00:15:24 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 01:03:08 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 01:48:08 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 02:31:25 2010] Joining segment hits
[Thu Jun 17 02:49:30 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 03:36:24 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 04:22:46 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 05:08:35 2010] Joining segment hits
[Thu Jun 17 05:27:50 2010] Reporting output tracks
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Run complete [21:47:19 elapsed]