[Mon Jun 14 16:36:16 2010] Beginning TopHat run (v1.0.13)
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[Mon Jun 14 16:36:16 2010] Preparing output location /projects/NBL/HS1801/61074AAXX_6/tophat_wj/
[Mon Jun 14 16:36:17 2010] Checking for Bowtie index files
[Mon Jun 14 16:36:17 2010] Checking for reference FASTA file
[Mon Jun 14 16:36:17 2010] Checking for Bowtie
	Bowtie version:		 0.12.5.0
[Mon Jun 14 16:36:17 2010] Checking reads
	seed length:	 75bp
	format:		 fastq
	quality scale:	 phred33 (default)
[Mon Jun 14 16:43:21 2010] Reading known junctions from GFF file
[Mon Jun 14 16:59:43 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 19:14:13 2010] Joining segment hits
	Splitting reads into 3 segments
[Mon Jun 14 19:23:04 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 20:52:47 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 22:22:50 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 23:53:16 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 02:07:55 2010] Joining segment hits
	Splitting reads into 3 segments
[Tue Jun 15 02:16:58 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 03:56:07 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 05:34:23 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 07:12:41 2010] Searching for junctions via segment mapping
[Tue Jun 15 07:37:37 2010] Retrieving sequences for splices
[Tue Jun 15 07:41:06 2010] Indexing splices
[Tue Jun 15 08:03:13 2010] Mapping reads against segment_juncs with Bowtie
[Tue Jun 15 08:56:52 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