[Wed Jun 16 11:10:03 2010] Beginning TopHat run (v1.0.13)
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[Wed Jun 16 11:10:03 2010] Preparing output location /projects/NBL/HS1797/616GYAAXX_1/tophat_wj/
[Wed Jun 16 11:10:03 2010] Checking for Bowtie index files
[Wed Jun 16 11:10:04 2010] Checking for reference FASTA file
[Wed Jun 16 11:10:04 2010] Checking for Bowtie
	Bowtie version:		 0.12.5.0
[Wed Jun 16 11:10:09 2010] Checking reads
	seed length:	 75bp
	format:		 fastq
	quality scale:	 phred33 (default)
[Wed Jun 16 11:20:53 2010] Reading known junctions from GFF file
[Wed Jun 16 11:36:24 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 14:27:20 2010] Joining segment hits
	Splitting reads into 3 segments
[Wed Jun 16 14:37:08 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 16:30:16 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 18:15:23 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 20:08:32 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 23:16:26 2010] Joining segment hits
	Splitting reads into 3 segments
[Wed Jun 16 23:38:39 2010] Mapping reads against hg18 with Bowtie
[Thu Jun 17 01:45:11 2010] Mapping reads against hg18 with Bowtie
[Thu Jun 17 03:28:38 2010] Mapping reads against hg18 with Bowtie
[Thu Jun 17 05:10:23 2010] Searching for junctions via segment mapping
[Thu Jun 17 05:33:46 2010] Retrieving sequences for splices
[Thu Jun 17 05:38:36 2010] Indexing splices
[Thu Jun 17 06:09:18 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 07:14:40 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 08:19:59 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 09:16:24 2010] Joining segment hits
[Thu Jun 17 10:14:40 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 11:40:01 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 12:38:45 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 13:37:27 2010] Joining segment hits
[Thu Jun 17 14:26:06 2010] Reporting output tracks
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Run complete [06:49:18 elapsed]