[Mon Jun 14 16:38:55 2010] Beginning TopHat run (v1.0.13)
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[Mon Jun 14 16:38:55 2010] Preparing output location /projects/NBL/HS1801/61074AAXX_7/tophat_wj/
[Mon Jun 14 16:38:55 2010] Checking for Bowtie index files
[Mon Jun 14 16:38:55 2010] Checking for reference FASTA file
[Mon Jun 14 16:38:55 2010] Checking for Bowtie
	Bowtie version:		 0.12.5.0
[Mon Jun 14 16:38:55 2010] Checking reads
	seed length:	 75bp
	format:		 fastq
	quality scale:	 phred33 (default)
[Mon Jun 14 16:46:32 2010] Reading known junctions from GFF file
[Mon Jun 14 17:03:03 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 19:22:47 2010] Joining segment hits
	Splitting reads into 3 segments
[Mon Jun 14 19:32:11 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 21:06:09 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 22:38:37 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 00:05:59 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 02:19:19 2010] Joining segment hits
	Splitting reads into 3 segments
[Tue Jun 15 02:28:27 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 04:09:14 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 05:51:05 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 07:30:13 2010] Searching for junctions via segment mapping
[Tue Jun 15 07:55:02 2010] Retrieving sequences for splices
[Tue Jun 15 07:58:33 2010] Indexing splices
[Tue Jun 15 08:20:18 2010] Mapping reads against segment_juncs with Bowtie
[Tue Jun 15 09:12:50 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