[Mon Jun 14 17:45:30 2010] Beginning TopHat run (v1.0.13)
-----------------------------------------------
[Mon Jun 14 17:45:30 2010] Preparing output location /projects/NBL/HS1797/616GYAAXX_2/tophat_wj/
[Mon Jun 14 17:45:30 2010] Checking for Bowtie index files
[Mon Jun 14 17:45:30 2010] Checking for reference FASTA file
[Mon Jun 14 17:45:30 2010] Checking for Bowtie
	Bowtie version:		 0.12.5.0
[Mon Jun 14 17:45:30 2010] Checking reads
	seed length:	 75bp
	format:		 fastq
	quality scale:	 phred33 (default)
[Mon Jun 14 17:54:11 2010] Reading known junctions from GFF file
[Mon Jun 14 18:08:39 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 21:07:11 2010] Joining segment hits
	Splitting reads into 3 segments
[Mon Jun 14 21:16:23 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 23:08:24 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 00:47:36 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 02:41:37 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 05:18:50 2010] Joining segment hits
	Splitting reads into 3 segments
[Tue Jun 15 05:26:17 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 07:08:29 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 08:42:39 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 10:18:52 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