CNVKit 0.9.9 Batch mode not producing CNS

[tbaker18]

Hello,

I saw there were previous issue #582. I am running CNVKit 0.9.9 batch mode with an existing reference and I noticed that none of my samples have the .cns output despite the segmentation step running. The log here is scrubbed, but contains the core contents

# name: cnvkit_wgs_batch
# command: cnvkit.py batch tumor.sorted.bam --method wgs --segment-method cbs --drop-low-coverage --processes 32 --reference my_reference.cnn --output-dir /some_dir/cnv
# error: None
/usr/local/lib/python3.8/dist-packages/skgenome/intersect.py:11: FutureWarning: pandas.Int64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead.
  from pandas import Int64Index
CNVkit 0.9.9
Wrote my_reference.target-tmp.bed with 566269 regions
Wrote my_reference.antitarget-tmp.bed with 0 regions
Running 1 samples in 32 processes (that's 32 processes per bam)
Running the CNVkit pipeline on tumor.sorted.bam ...
Processing reads in tumor.sorted.bam
Time: 728.938 seconds (3154732 reads/sec, 777 bins/sec)
Summary: #bins=566269, #reads=2299604335, mean=4060.9751, min=0.0, max=150472.23178807946 
Percent reads in regions: 80.866 (of 2843710027 mapped)
Wrote tumor.sorted.targetcoverage.cnn with 566269 regions
Skip processing tumor.sorted.bam with empty regions file my_reference.antitarget-tmp.bed
Wrote tumor.sorted.antitargetcoverage.cnn with 0 regions
Processing target: tumor.sorted
Keeping 563684 of 566269 bins
Correcting for GC bias...
Processing antitarget: tumor.sorted
Wrote tumor.sorted.cnr with 563684 regions
Segmenting tumor.sorted.cnr ...
Segmenting with method 'cbs', significance threshold 1e-06, in 32 processes
Dropped 3 / 9697 bins on chromosome chr4
Dropped 1 / 10086 bins on chromosome chr11
Dropped 1 / 13738 bins on chromosome chr15
Dropped 3 / 20963 bins on chromosome chr1

I understand I can manually perform segmenting and calling, but still would like to raise this issue so this could be fixed.

[tbaker18]

Located the issue. No need to resolve.

[eesiribloom]

what was the issue? I am having a similar problem

[bounlu]

@tbaker18 What was the issue? I am having a similar problem.

[tbaker18]

@bounlu I believe the issue was that R was not properly installed.