[Mon Jun 14 16:47:01 2010] Beginning TopHat run (v1.0.13)
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[Mon Jun 14 16:47:01 2010] Preparing output location /projects/NBL/HS1803/616GYAAXX_5/tophat_wj/
[Mon Jun 14 16:47:01 2010] Checking for Bowtie index files
[Mon Jun 14 16:47:01 2010] Checking for reference FASTA file
[Mon Jun 14 16:47:01 2010] Checking for Bowtie
	Bowtie version:		 0.12.5.0
[Mon Jun 14 16:47:02 2010] Checking reads
	seed length:	 75bp
	format:		 fastq
	quality scale:	 phred33 (default)
[Mon Jun 14 16:54:14 2010] Reading known junctions from GFF file
[Mon Jun 14 17:15:42 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 19:19:21 2010] Joining segment hits
	Splitting reads into 3 segments
[Mon Jun 14 19:27:31 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 20:50:04 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 22:19:15 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 23:50:03 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 01:57:20 2010] Joining segment hits
	Splitting reads into 3 segments
[Tue Jun 15 02:05:13 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 03:17:44 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 04:32:34 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 05:45:12 2010] Searching for junctions via segment mapping
[Tue Jun 15 06:06:06 2010] Retrieving sequences for splices
[Tue Jun 15 06:09:40 2010] Indexing splices
[Tue Jun 15 06:31:40 2010] Mapping reads against segment_juncs with Bowtie
[Tue Jun 15 07:17:21 2010] Mapping reads against segment_juncs with Bowtie
[Tue Jun 15 08:06:56 2010] Mapping reads against segment_juncs with Bowtie
[Tue Jun 15 08:52:37 2010] Joining segment hits
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 1493, in spliced_alignment
  File "/home/rcorbett/aligners/tophat/tophat-1.0.13/bin/tophat", line 1305, in join_mapped_segments
TypeError: 'str' object is not callable