[Mon Jun 14 17:00:33 2010] Beginning TopHat run (v1.0.13)
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[Mon Jun 14 17:00:33 2010] Preparing output location /projects/NBL/HS1797/616GYAAXX_1/tophat_wj/
[Mon Jun 14 17:00:33 2010] Checking for Bowtie index files
[Mon Jun 14 17:00:33 2010] Checking for reference FASTA file
[Mon Jun 14 17:00:33 2010] Checking for Bowtie
	Bowtie version:		 0.12.5.0
[Mon Jun 14 17:00:34 2010] Checking reads
	seed length:	 75bp
	format:		 fastq
	quality scale:	 phred33 (default)
[Mon Jun 14 17:08:59 2010] Reading known junctions from GFF file
[Mon Jun 14 17:27:38 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 20:19:54 2010] Joining segment hits
	Splitting reads into 3 segments
[Mon Jun 14 20:29:28 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 22:22:05 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 00:00:47 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 01:39:04 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 04:30:01 2010] Joining segment hits
	Splitting reads into 3 segments
[Tue Jun 15 04:37:42 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 06:08:07 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 07:39:07 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 09:09:42 2010] Searching for junctions via segment mapping
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 1435, in spliced_alignment
  File "/home/rcorbett/aligners/tophat/tophat-1.0.13/bin/tophat", line 1257, in junctions_from_segments
TypeError: 'str' object is not callable