[Mon Jun 14 15:11:29 2010] Beginning TopHat run (v1.0.13)
-----------------------------------------------
[Mon Jun 14 15:11:29 2010] Preparing output location /projects/NBL/HS1196/3153YAAXX_6/tophat_wj/
[Mon Jun 14 15:11:29 2010] Checking for Bowtie index files
[Mon Jun 14 15:11:29 2010] Checking for reference FASTA file
[Mon Jun 14 15:11:29 2010] Checking for Bowtie
	Bowtie version:		 0.12.5.0
[Mon Jun 14 15:11:29 2010] Checking reads
	seed length:	 50bp
	format:		 fastq
	quality scale:	 phred33 (default)
[Mon Jun 14 15:14:18 2010] Reading known junctions from GFF file
[Mon Jun 14 15:24:54 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 16:42:19 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 17:00:49 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 17:39:08 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 18:17:25 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 19:27:41 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 19:31:03 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 20:16:44 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 20:57:33 2010] Searching for junctions via segment mapping
[Mon Jun 14 21:18:27 2010] Retrieving sequences for splices
[Mon Jun 14 21:22:05 2010] Indexing splices
[Mon Jun 14 21:33:45 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 21:47:48 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 22:00:46 2010] Joining segment hits
[Mon Jun 14 22:08:15 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 22:24:08 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 22:38:48 2010] Joining segment hits
[Mon Jun 14 22:42:44 2010] Reporting output tracks
-----------------------------------------------
Run complete [07:54:15 elapsed]