[Mon Jun 14 16:53:26 2010] Beginning TopHat run (v1.0.13)
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[Mon Jun 14 16:53:26 2010] Preparing output location /projects/NBL/HS1799/61074AAXX_4/tophat_wj/
[Mon Jun 14 16:53:27 2010] Checking for Bowtie index files
[Mon Jun 14 16:53:27 2010] Checking for reference FASTA file
[Mon Jun 14 16:53:27 2010] Checking for Bowtie
	Bowtie version:		 0.12.5.0
[Mon Jun 14 16:53:27 2010] Checking reads
	seed length:	 75bp
	format:		 fastq
	quality scale:	 phred33 (default)
[Mon Jun 14 17:01:27 2010] Reading known junctions from GFF file
[Mon Jun 14 17:25:23 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 19:41:19 2010] Joining segment hits
	Splitting reads into 3 segments
[Mon Jun 14 19:48:51 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 21:05:58 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 22:23:47 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 23:41:32 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 01:50:28 2010] Joining segment hits
	Splitting reads into 3 segments
[Tue Jun 15 01:58:10 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 03:22:57 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 04:45:19 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 06:05:57 2010] Searching for junctions via segment mapping
[Tue Jun 15 06:24:07 2010] Retrieving sequences for splices
[Tue Jun 15 06:27:31 2010] Indexing splices
[Tue Jun 15 06:47:05 2010] Mapping reads against segment_juncs with Bowtie
[Tue Jun 15 07:31:56 2010] Mapping reads against segment_juncs with Bowtie
[Tue Jun 15 08:16:00 2010] Mapping reads against segment_juncs with Bowtie
[Tue Jun 15 08:58:17 2010] Joining segment hits
Traceback (most recent call last):
  File "/home/rcorbett/aligners/tophat/tophat-1.0.13/bin/tophat", line 1636, in ?
  File "/home/rcorbett/aligners/tophat/tophat-1.0.13/bin/tophat", line 1596, in main
  File "/home/rcorbett/aligners/tophat/tophat-1.0.13/bin/tophat", line 1493, in spliced_alignment
  File "/home/rcorbett/aligners/tophat/tophat-1.0.13/bin/tophat", line 1305, in join_mapped_segments
TypeError: 'str' object is not callable