[Mon Jun 14 15:13:11 2010] Beginning TopHat run (v1.0.13)
-----------------------------------------------
[Mon Jun 14 15:13:11 2010] Preparing output location /projects/NBL/HS1195/30TTYAAXX_5/tophat_wj/
[Mon Jun 14 15:13:11 2010] Checking for Bowtie index files
[Mon Jun 14 15:13:11 2010] Checking for reference FASTA file
[Mon Jun 14 15:13:11 2010] Checking for Bowtie
	Bowtie version:		 0.12.5.0
[Mon Jun 14 15:13:11 2010] Checking reads
	seed length:	 50bp
	format:		 fastq
	quality scale:	 phred33 (default)
[Mon Jun 14 15:17:25 2010] Reading known junctions from GFF file
[Mon Jun 14 15:27:36 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 16:51:27 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 17:00:01 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 17:39:51 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 18:12:09 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 18:55:11 2010] Joining segment hits
	Splitting reads into 2 segments
[Mon Jun 14 19:04:30 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 19:31:12 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 20:42:23 2010] Searching for junctions via segment mapping
[Mon Jun 14 22:36:26 2010] Retrieving sequences for splices
[Mon Jun 14 22:42:54 2010] Indexing splices
[Mon Jun 14 23:19:53 2010] Mapping reads against segment_juncs with Bowtie
[Mon Jun 14 23:57:31 2010] Mapping reads against segment_juncs with Bowtie
[Tue Jun 15 00:28:04 2010] Joining segment hits
[Tue Jun 15 00:47:45 2010] Mapping reads against segment_juncs with Bowtie
[Tue Jun 15 01:15:55 2010] Mapping reads against segment_juncs with Bowtie
[Tue Jun 15 02:12:42 2010] Joining segment hits
[Tue Jun 15 02:26:08 2010] Reporting output tracks
-----------------------------------------------
Run complete [11:55:30 elapsed]