[Mon Jun 14 16:50:14 2010] Beginning TopHat run (v1.0.13)
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[Mon Jun 14 16:50:14 2010] Preparing output location /projects/NBL/HS1795/700B4AAXX_2/tophat_wj/
[Mon Jun 14 16:50:14 2010] Checking for Bowtie index files
[Mon Jun 14 16:50:14 2010] Checking for reference FASTA file
[Mon Jun 14 16:50:14 2010] Checking for Bowtie
	Bowtie version:		 0.12.5.0
[Mon Jun 14 16:50:14 2010] Checking reads
	seed length:	 75bp
	format:		 fastq
	quality scale:	 phred33 (default)
[Mon Jun 14 17:01:12 2010] Reading known junctions from GFF file
[Mon Jun 14 17:27:35 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 20:06:10 2010] Joining segment hits
	Splitting reads into 3 segments
[Mon Jun 14 20:15:41 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 22:29:50 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 00:52:36 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 02:34:12 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 04:57:10 2010] Joining segment hits
	Splitting reads into 3 segments
[Tue Jun 15 05:05:16 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 07:08:17 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 09:03:40 2010] Mapping reads against hg18 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 1410, in spliced_alignment
  File "/home/rcorbett/aligners/tophat/tophat-1.0.13/bin/tophat", line 878, in bowtie
TypeError: 'str' object is not callable