bunzip2: Can't open input file /projects/NBL/HS1803/616GYAAXX_5/tophat_wj/616GYAAXX_5_2_concat_qseq.txt.bz2: No such file or directory.

[Wed Jun 16 10:53:46 2010] Beginning TopHat run (v1.0.13)
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[Wed Jun 16 10:53:46 2010] Preparing output location /projects/NBL/HS1803/616GYAAXX_5/tophat_wj/
[Wed Jun 16 10:53:46 2010] Checking for Bowtie index files
[Wed Jun 16 10:53:47 2010] Checking for reference FASTA file
[Wed Jun 16 10:53:47 2010] Checking for Bowtie
	Bowtie version:		 0.12.5.0
[Wed Jun 16 10:53:47 2010] Checking reads
	seed length:	 75bp
	format:		 fastq
	quality scale:	 phred33 (default)
[Wed Jun 16 11:01:08 2010] Reading known junctions from GFF file
[Wed Jun 16 11:20:24 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 13:26:37 2010] Joining segment hits
	Splitting reads into 3 segments
[Wed Jun 16 13:35:56 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 15:02:30 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 16:34:36 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 18:03:18 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 20:36:11 2010] Joining segment hits
	Splitting reads into 3 segments
[Wed Jun 16 21:28:33 2010] Mapping reads against hg18 with Bowtie
[Wed Jun 16 22:50:17 2010] Mapping reads against hg18 with Bowtie
[Thu Jun 17 00:10:23 2010] Mapping reads against hg18 with Bowtie
[Thu Jun 17 01:28:32 2010] Searching for junctions via segment mapping
[Thu Jun 17 01:51:23 2010] Retrieving sequences for splices
[Thu Jun 17 01:55:36 2010] Indexing splices
[Thu Jun 17 02:19:07 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 03:07:18 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 03:58:27 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 04:45:53 2010] Joining segment hits
[Thu Jun 17 05:13:43 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 05:59:06 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 06:45:34 2010] Mapping reads against segment_juncs with Bowtie
[Thu Jun 17 07:29:29 2010] Joining segment hits
[Thu Jun 17 08:40:13 2010] Reporting output tracks
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Run complete [03:34:49 elapsed]