segment - ValueError: cannot convert float NaN to integer

[pontushojer]

I am running cnvkit segment with the HMM method on a WGS .cnr file and running into the following error:

/usr/local/lib/python3.10/site-packages/cnvlib/descriptives.py:240: RuntimeWarning: invalid value enco>
  var = np.average((a - mean) ** 2, weights=weights)
Traceback (most recent call last):
  File "/usr/local/bin/cnvkit.py", line 10, in <module>
    sys.exit(main())
  File "/usr/local/lib/python3.10/site-packages/cnvlib/cnvkit.py", line 10, in main
    args.func(args)
  File "/usr/local/lib/python3.10/site-packages/cnvlib/commands.py", line 994, in _cmd_segment
    results = segmentation.do_segmentation(
  File "/usr/local/lib/python3.10/site-packages/cnvlib/segmentation/__init__.py", line 62, in do_segme>
    cna = _do_segmentation(
  File "/usr/local/lib/python3.10/site-packages/cnvlib/segmentation/__init__.py", line 180, in _do_seg>
    segarr = hmm.segment_hmm(filtered_cn, method, threshold, variants)
  File "/usr/local/lib/python3.10/site-packages/cnvlib/segmentation/hmm.py", line 39, in segment_hmm
    cnarr["log2"] = cnarr.smooth_log2()  # window)
  File "/usr/local/lib/python3.10/site-packages/cnvlib/cnary.py", line 506, in smooth_log2
    bandwidth = smoothing.guess_window_size(
  File "/usr/local/lib/python3.10/site-packages/cnvlib/smoothing.py", line 128, in guess_window_size
    width = max(3, int(round(width)))
ValueError: cannot convert float NaN to integer

This is the command I used:

cnvkit.py segment {input.cnr} -m hmm -t 1e-6 -o {output.cns} &> {log}

The .cnr is from a low coverage (<1X) dataset.

cnvkit version: 0.9.10

[etal]

Is this issue still present in the latest release, v0.9.13? The HMM code changed a lot, so it might have been fixed.