I am trying to run Tophat with the simple basic command (using no options) and have done so successfully before but now when I try to run it, I get the following error:
[Mon Aug 16 10:59:32 2010] Mapping reads against b_taurus with Bowtie
[Mon Aug 16 11:34:47 2010] Mapping reads against b_taurus with Bowtie
[Mon Aug 16 12:06:51 2010] Searching for junctions via segment mapping
[Mon Aug 16 12:12:04 2010] Retrieving sequences for splices
[Mon Aug 16 12:14:18 2010] Indexing splices
[Mon Aug 16 12:14:19 2010] Mapping reads against segment_juncs with Bowtie
[Mon Aug 16 12:15:06 2010] Mapping reads against segment_juncs with Bowtie
[Mon Aug 16 12:15:53 2010] Joining segment hits
[FAILED]
Error: Segment join failed with err = 1
Traceback (most recent call last):
File "/raid/warehouse/tophat-1.0.13/bin/tophat", line 1635, in ?
sys.exit(main())
File "/raid/warehouse/tophat-1.0.13/bin/tophat", line 1595, in main
user_supplied_juncs)
File "/raid/warehouse/tophat-1.0.13/bin/tophat", line 1492, in spliced_alignment
mapped_reads)
File "/raid/warehouse/tophat-1.0.13/bin/tophat", line 1299, in join_mapped_segments
exit(1)
TypeError: 'str' object is not callable
Any help would be appreciated, thanks.
[Mon Aug 16 10:59:32 2010] Mapping reads against b_taurus with Bowtie
[Mon Aug 16 11:34:47 2010] Mapping reads against b_taurus with Bowtie
[Mon Aug 16 12:06:51 2010] Searching for junctions via segment mapping
[Mon Aug 16 12:12:04 2010] Retrieving sequences for splices
[Mon Aug 16 12:14:18 2010] Indexing splices
[Mon Aug 16 12:14:19 2010] Mapping reads against segment_juncs with Bowtie
[Mon Aug 16 12:15:06 2010] Mapping reads against segment_juncs with Bowtie
[Mon Aug 16 12:15:53 2010] Joining segment hits
[FAILED]
Error: Segment join failed with err = 1
Traceback (most recent call last):
File "/raid/warehouse/tophat-1.0.13/bin/tophat", line 1635, in ?
sys.exit(main())
File "/raid/warehouse/tophat-1.0.13/bin/tophat", line 1595, in main
user_supplied_juncs)
File "/raid/warehouse/tophat-1.0.13/bin/tophat", line 1492, in spliced_alignment
mapped_reads)
File "/raid/warehouse/tophat-1.0.13/bin/tophat", line 1299, in join_mapped_segments
exit(1)
TypeError: 'str' object is not callable
Any help would be appreciated, thanks.
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