[Mon Jun 14 17:07:36 2010] Beginning TopHat run (v1.0.13)
-----------------------------------------------
[Mon Jun 14 17:07:36 2010] Preparing output location /projects/NBL/HS1803/616GYAAXX_4/tophat_wj/
[Mon Jun 14 17:07:36 2010] Checking for Bowtie index files
[Mon Jun 14 17:07:36 2010] Checking for reference FASTA file
[Mon Jun 14 17:07:36 2010] Checking for Bowtie
	Bowtie version:		 0.12.5.0
[Mon Jun 14 17:07:36 2010] Checking reads
	seed length:	 75bp
	format:		 fastq
	quality scale:	 phred33 (default)
[Mon Jun 14 17:14:57 2010] Reading known junctions from GFF file
[Mon Jun 14 17:35:56 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 19:51:33 2010] Joining segment hits
	Splitting reads into 3 segments
[Mon Jun 14 19:59:11 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 21:19:03 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 22:36:01 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 23:50:49 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 01:52:59 2010] Joining segment hits
	Splitting reads into 3 segments
[Tue Jun 15 02:00:23 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 03:20:11 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 04:42:09 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 06:00:56 2010] Searching for junctions via segment mapping
[Tue Jun 15 06:20:46 2010] Retrieving sequences for splices
[Tue Jun 15 06:24:14 2010] Indexing splices
[Tue Jun 15 06:45:08 2010] Mapping reads against segment_juncs with Bowtie
[Tue Jun 15 07:30:39 2010] Mapping reads against segment_juncs with Bowtie
[Tue Jun 15 08:14:53 2010] Mapping reads against segment_juncs with Bowtie
[Tue Jun 15 08:56:12 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