[Mon Jun 14 16:27:46 2010] Beginning TopHat run (v1.0.13)
-----------------------------------------------
[Mon Jun 14 16:27:46 2010] Preparing output location /projects/NBL/HS1799/61074AAXX_3/tophat_wj/
[Mon Jun 14 16:27:46 2010] Checking for Bowtie index files
[Mon Jun 14 16:27:46 2010] Checking for reference FASTA file
[Mon Jun 14 16:27:46 2010] Checking for Bowtie
	Bowtie version:		 0.12.5.0
[Mon Jun 14 16:27:46 2010] Checking reads
	seed length:	 75bp
	format:		 fastq
	quality scale:	 phred33 (default)
[Mon Jun 14 16:34:33 2010] Reading known junctions from GFF file
[Mon Jun 14 16:50:33 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 19:04:29 2010] Joining segment hits
	Splitting reads into 3 segments
[Mon Jun 14 19:12:22 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 20:28:49 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 21:47:06 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 23:06:42 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 01:22:40 2010] Joining segment hits
	Splitting reads into 3 segments
[Tue Jun 15 01:30:17 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 02:55:06 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 04:16:17 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 05:36:39 2010] Searching for junctions via segment mapping
[Tue Jun 15 05:55:08 2010] Retrieving sequences for splices
[Tue Jun 15 05:58:36 2010] Indexing splices
[Tue Jun 15 06:19:40 2010] Mapping reads against segment_juncs with Bowtie
[Tue Jun 15 07:05:20 2010] Mapping reads against segment_juncs with Bowtie
[Tue Jun 15 07:50:36 2010] Mapping reads against segment_juncs with Bowtie
[Tue Jun 15 08:34:08 2010] Joining segment hits
[Tue Jun 15 08:44:21 2010] Mapping reads against segment_juncs with Bowtie
[Tue Jun 15 09:31:45 2010] Mapping reads against segment_juncs with Bowtie
[Tue Jun 15 10:19:39 2010] Mapping reads against segment_juncs with Bowtie
[Tue Jun 15 11:05:20 2010] Joining segment hits
[Tue Jun 15 11:16:17 2010] Reporting output tracks
-----------------------------------------------
Run complete [21:52:16 elapsed]