[Mon Jun 14 16:44:36 2010] Beginning TopHat run (v1.0.13)
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[Mon Jun 14 16:44:36 2010] Preparing output location /projects/NBL/HS1801/61074AAXX_8/tophat_wj/
[Mon Jun 14 16:44:36 2010] Checking for Bowtie index files
[Mon Jun 14 16:44:36 2010] Checking for reference FASTA file
[Mon Jun 14 16:44:36 2010] Checking for Bowtie
	Bowtie version:		 0.12.5.0
[Mon Jun 14 16:44:37 2010] Checking reads
	seed length:	 75bp
	format:		 fastq
	quality scale:	 phred33 (default)
[Mon Jun 14 16:52:05 2010] Reading known junctions from GFF file
[Mon Jun 14 17:08:31 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 19:27:57 2010] Joining segment hits
	Splitting reads into 3 segments
[Mon Jun 14 19:36:10 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 21:06:20 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 22:38:46 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 00:07:10 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 02:16:20 2010] Joining segment hits
	Splitting reads into 3 segments
[Tue Jun 15 02:24:31 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 04:02:12 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 05:41:10 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 07:18:45 2010] Searching for junctions via segment mapping
[Tue Jun 15 07:43:20 2010] Retrieving sequences for splices
[Tue Jun 15 07:46:44 2010] Indexing splices
[Tue Jun 15 08:07:42 2010] Mapping reads against segment_juncs with Bowtie
[Tue Jun 15 08:59:29 2010] Mapping reads against segment_juncs with Bowtie
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 1481, in spliced_alignment
  File "/home/rcorbett/aligners/tophat/tophat-1.0.13/bin/tophat", line 878, in bowtie
TypeError: 'str' object is not callable