Tophat on Mac

[RAS55331]

I am running tophat on a 12 core, 64gb ram Mac OSX 10.6.8, about 60M sequences against hg19. Things seem to go ok for about 3 hours but then I get to the 'Searching for junctions via segment mapping' step (segment_juncs) and the process hangs indefinitely with a single processor pegged at 100%, less than half the ram in use. Killing the process returns:

File "/Users/informatics/tophat-1.4.1.OSX_x86_64/tophat", line 3063, in <module>
sys.exit(main())
File "/Users/informatics/tophat-1.4.1.OSX_x86_64/tophat", line 3029, in main
user_supplied_deletions)
File "/Users/informatics/tophat-1.4.1.OSX_x86_64/tophat", line 2670, in spliced_alignment
ref_fasta)
File "/Users/informatics/tophat-1.4.1.OSX_x86_64/tophat", line 2196, in junctions_from_segments
stderr=segj_log)
File "/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/subprocess.py", line 444, in call
return Popen(*popenargs, **kwargs).wait()
File "/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/subprocess.py", line 1137, in wait
pid, sts = os.waitpid(self.pid, 0)

Has anyone else had this problem?

[KHooks]

Me. Tried few times with different settings but it always hangs in the same place just as you described. Did you got a solution yet? Now I'm trying the tophat2 hoping freezing will disappear.

[RAS55331]

I think it is simply a bottleneck in the process. I got it to complete using the -M and -GTF options. Takes about 10 hours but that's not too bad. We're switching to Tophat2 too, hope it goes well for you.

[biznatch]

It's most likely working as intended. That step is single threaded and just takes a long time, especially depending what options you are using when running Tophat.