[Mon Jun 14 17:34:15 2010] Beginning TopHat run (v1.0.13)
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[Mon Jun 14 17:34:15 2010] Preparing output location /projects/NBL/HS1799/61074AAXX_5/tophat_wj/
[Mon Jun 14 17:34:16 2010] Checking for Bowtie index files
[Mon Jun 14 17:34:16 2010] Checking for reference FASTA file
[Mon Jun 14 17:34:16 2010] Checking for Bowtie
	Bowtie version:		 0.12.5.0
[Mon Jun 14 17:34:16 2010] Checking reads
	seed length:	 75bp
	format:		 fastq
	quality scale:	 phred33 (default)
[Mon Jun 14 17:41:40 2010] Reading known junctions from GFF file
[Mon Jun 14 17:53:35 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 20:11:58 2010] Joining segment hits
	Splitting reads into 3 segments
[Mon Jun 14 20:20:09 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 21:40:31 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 22:58:18 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 00:15:52 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 02:28:08 2010] Joining segment hits
	Splitting reads into 3 segments
[Tue Jun 15 02:35:21 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 03:56:25 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 05:19:44 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 06:41:01 2010] Searching for junctions via segment mapping
[Tue Jun 15 06:59:42 2010] Retrieving sequences for splices
[Tue Jun 15 07:03:09 2010] Indexing splices
[Tue Jun 15 07:22:02 2010] Mapping reads against segment_juncs with Bowtie
[Tue Jun 15 08:07:44 2010] Mapping reads against segment_juncs with Bowtie
[Tue Jun 15 08:53:10 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