etal / cnvkit

Copy number variant detection from targeted DNA sequencing
http://cnvkit.readthedocs.org
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Improper post-processing of segment [bug] #893

Open GACGAMA opened 1 week ago

GACGAMA commented 1 week ago

I'm segmenting my files with a vcf, with cnvkit version 0.9.11 from conda

I'm getting the following error with the segment command:


Segment chr1:258166-121975959 on allele freqs for 91 additional breakpoints
Traceback (most recent call last):
  File "/home/ggama1/.conda/envs/cnvkit/bin/cnvkit.py", line 10, in <module>
    sys.exit(main())
  File "/home/ggama1/.conda/envs/cnvkit/lib/python3.10/site-packages/cnvlib/cnvkit.py", line 10, in main
    args.func(args)
  File "/home/ggama1/.conda/envs/cnvkit/lib/python3.10/site-packages/cnvlib/commands.py", line 1022, in _cmd_segment
    results = segmentation.do_segmentation(
  File "/home/ggama1/.conda/envs/cnvkit/lib/python3.10/site-packages/cnvlib/segmentation/__init__.py", line 81, in do_segmentation
    rets = list(
  File "/home/ggama1/.conda/envs/cnvkit/lib/python3.10/site-packages/cnvlib/segmentation/__init__.py", line 126, in _ds
    return _do_segmentation(*args)
  File "/home/ggama1/.conda/envs/cnvkit/lib/python3.10/site-packages/cnvlib/segmentation/__init__.py", line 231, in _do_segmentation
    newsegs = [
  File "/home/ggama1/.conda/envs/cnvkit/lib/python3.10/site-packages/cnvlib/segmentation/__init__.py", line 232, in <listcomp>
    hmm.variants_in_segment(subvarr, segment)
  File "/home/ggama1/.conda/envs/cnvkit/lib/python3.10/site-packages/cnvlib/segmentation/hmm.py", line 247, in variants_in_segment
    raise RuntimeError(
RuntimeError: Improper post-processing of segment Pandas(chromosome='chr1', start=258166, end=121975959, gene='-', log2=-0.0345478627806626, probes=12306) -- 1 bins start >= end:
   chromosome     start       end gene      log2  probes
41       chr1  26282391  26282384    - -0.034548      14

This is related to #513 buy I tought it was already patched from previous versions