I recently installed cnvkit locally on to a computing cluster by cloning it from github (0.8.6dev0), building, and installing it. I then pip installed all of the dependencies and installed the necessary packages in R. I then tried to test the installation as explained on github, but failed at the segment call with the following error:
[nbay13@n7157 test]$ make python ../cnvkit.py segment -p 2 --drop-low-coverage -t .01 build/p2-5_5.cnr -o build/p2-5_5.cns Traceback (most recent call last): File "../cnvkit.py", line 13, in <module> args.func(args) File "/u/home/n/nbay13/cnvkit/cnvlib/commands.py", line 597, in _cmd_segment processes=args.processes) File "/u/home/n/nbay13/cnvkit/cnvlib/segmentation/__init__.py", line 42, in do_segmentation for _, ca in cnarr.by_chromosome()))) File "/u/home/n/nbay13/.local/lib/python2.7/site-packages/concurrent/futures/_base.py", line 581, in result_iterator yield future.result() File "/u/home/n/nbay13/.local/lib/python2.7/site-packages/concurrent/futures/_base.py", line 405, in result return self.__get_result() File "/u/home/n/nbay13/.local/lib/python2.7/site-packages/concurrent/futures/_base.py", line 357, in __get_result raise type(self._exception), self._exception, self._traceback ValueError: Unexpected dataframe contents: NULL byte detected. This byte cannot be processed in Python's native csv library at the moment, so please pass in engine='c' instead "p2-5_5" "chr1" 142517943 249066405 671 0.00824754582746605
I have similarly tried to segment my own data without multiprocessing to no avail.
Switching the method to haar works, but both PSCBS and Lasso do not. So it seems that the problem might have to do with R (my version currently is 3.3.0, but I've also tried 3.2.3). If possible I would like to use PSCBS.
Any help would be much appreciated.