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