[Mon Jun 14 17:04:55 2010] Beginning TopHat run (v1.0.13)
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[Mon Jun 14 17:04:55 2010] Preparing output location /projects/NBL/HS1795/700B4AAXX_3/tophat_wj/
[Mon Jun 14 17:04:55 2010] Checking for Bowtie index files
[Mon Jun 14 17:04:55 2010] Checking for reference FASTA file
[Mon Jun 14 17:04:55 2010] Checking for Bowtie
	Bowtie version:		 0.12.5.0
[Mon Jun 14 17:04:55 2010] Checking reads
	seed length:	 75bp
	format:		 fastq
	quality scale:	 phred33 (default)
[Mon Jun 14 17:12:03 2010] Reading known junctions from GFF file
[Mon Jun 14 17:37:14 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 20:01:49 2010] Joining segment hits
	Splitting reads into 3 segments
[Mon Jun 14 20:10:32 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 21:36:33 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 23:05:26 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 00:29:58 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 02:39:11 2010] Joining segment hits
	Splitting reads into 3 segments
[Tue Jun 15 02:46:49 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 04:10:55 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 05:35:32 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 07:00:02 2010] Searching for junctions via segment mapping
[Tue Jun 15 07:21:15 2010] Retrieving sequences for splices
[Tue Jun 15 07:24:43 2010] Indexing splices
[Tue Jun 15 07:45:26 2010] Mapping reads against segment_juncs with Bowtie
[Tue Jun 15 08:36:07 2010] Mapping reads against segment_juncs with Bowtie
[Tue Jun 15 09:25:39 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