[Mon Jun 14 15:21:23 2010] Beginning TopHat run (v1.0.13)
-----------------------------------------------
[Mon Jun 14 15:21:23 2010] Preparing output location /projects/NBL/HS1198/30UBRAAXX_6/tophat_wj/
[Mon Jun 14 15:21:23 2010] Checking for Bowtie index files
[Mon Jun 14 15:21:23 2010] Checking for reference FASTA file
[Mon Jun 14 15:21:23 2010] Checking for Bowtie
	Bowtie version:		 0.12.5.0
[Mon Jun 14 15:21:23 2010] Checking reads
	seed length:	 50bp
	format:		 fastq
	quality scale:	 phred33 (default)
[Mon Jun 14 15:24:14 2010] Reading known junctions from GFF file
[Mon Jun 14 15:31:16 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 16:47:29 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 16:53:58 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 17:35:21 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 18:14:29 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 19:22:18 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 19:26:26 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 20:14:07 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 20:59:28 2010] Searching for junctions via segment mapping
[Mon Jun 14 21:25:33 2010] Retrieving sequences for splices
[Mon Jun 14 21:30:13 2010] Indexing splices
[Mon Jun 14 21:41:55 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 21:58:58 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 22:13:22 2010] Joining segment hits
[Mon Jun 14 22:22:03 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 22:38:54 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 22:54:06 2010] Joining segment hits
[Mon Jun 14 23:03:28 2010] Reporting output tracks
-----------------------------------------------
Run complete [09:01:35 elapsed]