Error : run cnvkit from bam

Question

[reany]

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

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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'>, ())

---

[Amitm]

Hi, If you post the cmd you actually ran, that might be more helpful in finding what might be wrong.

[reany]

sorry. Edit the post again. Maybe the error was relevant to subprocesses. I am not sure.

[Amitm]

Hi, There seems to be an additional space after the -r argument. Can you remove the extra space and run again. Not sure though if this is the main reason, but try

[reany]

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.

[Amitm]

If it helps, I used the set-up below and it did work fine.

cnvkit.py batch \
BAM_files /path/to/tumour/*.bam \
--normal /path/to/germline/*.bam \
--drop-low-coverage \
-p 12 \
--targets my_CNVKit_Targets_AutosomesOnly.bed \
--antitargets my_CNVKit_AntiTargets.bed \
--fasta /path/to/human_g1k_v37.fasta \
--access access-5k-mappable_grch37_AutosomesOnly.bed \
--output-reference my_reference.cnn \
--output-dir results/ \
--diagram \
--scatter

[reany]

Thanks for your reply. I will try.

[reany]

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.