[Mon Jun 14 16:32:58 2010] Beginning TopHat run (v1.0.13)
-----------------------------------------------
[Mon Jun 14 16:32:58 2010] Preparing output location /projects/NBL/HS1799/61B1HAAXX_7/tophat_wj/
[Mon Jun 14 16:32:58 2010] Checking for Bowtie index files
[Mon Jun 14 16:32:59 2010] Checking for reference FASTA file
[Mon Jun 14 16:32:59 2010] Checking for Bowtie
	Bowtie version:		 0.12.5.0
[Mon Jun 14 16:32:59 2010] Checking reads
	seed length:	 75bp
	format:		 fastq
	quality scale:	 phred33 (default)
[Mon Jun 14 16:39:37 2010] Reading known junctions from GFF file
[Mon Jun 14 16:57:35 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 19:13:25 2010] Joining segment hits
	Splitting reads into 3 segments
[Mon Jun 14 19:21:50 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 20:48:32 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 22:15:06 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 23:36:15 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 01:43:24 2010] Joining segment hits
	Splitting reads into 3 segments
[Tue Jun 15 01:51:04 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 03:04:35 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 04:18:33 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 05:33:22 2010] Searching for junctions via segment mapping
[Tue Jun 15 05:52:22 2010] Retrieving sequences for splices
[Tue Jun 15 05:55:52 2010] Indexing splices
[Tue Jun 15 06:17:17 2010] Mapping reads against segment_juncs with Bowtie
[Tue Jun 15 07:03:17 2010] Mapping reads against segment_juncs with Bowtie
[Tue Jun 15 07:49:00 2010] Mapping reads against segment_juncs with Bowtie
[Tue Jun 15 08:32:47 2010] Joining segment hits
[Tue Jun 15 08:43:00 2010] Mapping reads against segment_juncs with Bowtie
[Tue Jun 15 09:26:29 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