Entering edit mode
4.8 years ago
reany ▴ 50
I get an error when i run cnvkit from bam file, but run successfully from fastq file in virtual machine. Hoping someone will give a hand, thankx.The error and script like blow:
cnvkit.py batch RNDHD701_180904_041701.bam -r my.reference.cnn -d RNDHD701P04_180904_041701_ANALYSIS/cnv -p 16
Exception in thread Thread-2: Traceback (most recent call last): File "/usr/lib64/python2.7/threading.py", line 812, in __bootstrap_inner self.run() File "/usr/lib64/python2.7/threading.py", line 765, in run self.__target(*self.__args, **self.__kwargs) File "/mnt/pipeline-programs/Python_packages/python/lib/python2.7/site-packages/concurrent/futures/process.py", line 208, in _queue_management_worker result_item = result_queue.get(block=True) File "/usr/lib64/python2.7/multiprocessing/queues.py", line 117, in get res = self._recv() TypeError: ('__init__() takes exactly 2 arguments (1 given)', <class 'pysam.utils.SamtoolsError'>, ())
Hi, If you post the cmd you actually ran, that might be more helpful in finding what might be wrong.
sorry. Edit the post again. Maybe the error was relevant to subprocesses. I am not sure.
Hi, There seems to be an additional space after the
-rargument. Can you remove the extra space and run again. Not sure though if this is the main reason, but try
Try again and get the same error. Interestingly, cnvkit will work well in the pipeline starting with fastq file,even though it has the same cmd in CNV calling.
If it helps, I used the set-up below and it did work fine.
Thanks for your reply. I will try.
I have got the question. The index file was old than bam, cnvkit will index bam and rewrite the bai file but failed because of privileged access.