[Mon Jun 14 16:29:55 2010] Beginning TopHat run (v1.0.13)
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[Mon Jun 14 16:29:55 2010] Preparing output location /projects/NBL/HS1801/61B1HAAXX_8/tophat_wj/
[Mon Jun 14 16:29:55 2010] Checking for Bowtie index files
[Mon Jun 14 16:29:55 2010] Checking for reference FASTA file
[Mon Jun 14 16:29:55 2010] Checking for Bowtie
	Bowtie version:		 0.12.5.0
[Mon Jun 14 16:29:56 2010] Checking reads
	seed length:	 75bp
	format:		 fastq
	quality scale:	 phred33 (default)
[Mon Jun 14 16:35:37 2010] Reading known junctions from GFF file
[Mon Jun 14 16:52:07 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 18:46:23 2010] Joining segment hits
	Splitting reads into 3 segments
[Mon Jun 14 19:02:10 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 20:14:04 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 21:27:35 2010] Mapping reads against hg18 with Bowtie
[Mon Jun 14 22:38:44 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 00:30:15 2010] Joining segment hits
	Splitting reads into 3 segments
[Tue Jun 15 00:38:06 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 01:53:51 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 03:09:22 2010] Mapping reads against hg18 with Bowtie
[Tue Jun 15 04:24:59 2010] Searching for junctions via segment mapping
[Tue Jun 15 04:46:30 2010] Retrieving sequences for splices
[Tue Jun 15 04:49:58 2010] Indexing splices
[Tue Jun 15 05:11:02 2010] Mapping reads against segment_juncs with Bowtie
[Tue Jun 15 05:53:37 2010] Mapping reads against segment_juncs with Bowtie
[Tue Jun 15 06:36:15 2010] Mapping reads against segment_juncs with Bowtie
[Tue Jun 15 07:16:52 2010] Joining segment hits
[Tue Jun 15 07:26:20 2010] Mapping reads against segment_juncs with Bowtie
[Tue Jun 15 08:11:14 2010] Mapping reads against segment_juncs with Bowtie
[Tue Jun 15 08:55:42 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