cnvkit.py segment error

[l0ka]

Hi, I'm running CNVkit on RNAseq data. I managed to run import-rna and got the *.cnr files. Now I'm trying to run the segment step and I'm experiencing the following error:

cnvkit.py segment \
    --output BIT5.cns \
    --method cbs \
    --processes 0 \
    --smooth-cbs \
    BIT5.cnr
Segmenting with method 'cbs', significance threshold 0.0001, in 0 processes
Dropped 96 / 1270 bins on chromosome 1
Dropped 89 / 543 bins on chromosome 2
Dropped 84 / 1017 bins on chromosome 1
Dropped 263 / 1006 bins on chromosome 2
Dropped 41 / 1081 bins on chromosome 3
Dropped 7 / 241 bins on chromosome 3
Dropped 7 / 175 bins on chromosome 4
Dropped 55 / 650 bins on chromosome 4
Dropped 10 / 369 bins on chromosome 6
Dropped 9 / 198 bins on chromosome 5
Dropped 25 / 736 bins on chromosome 6
Dropped 10 / 418 bins on chromosome 7
Dropped 34 / 914 bins on chromosome 5
Dropped 28 / 828 bins on chromosome 7
Dropped 13 / 304 bins on chromosome 8
Dropped 55 / 533 bins on chromosome 8
Dropped 1 / 280 bins on chromosome 9
Dropped 12 / 659 bins on chromosome 9
Dropped 1 / 172 bins on chromosome 10
Dropped 17 / 412 bins on chromosome 11
Dropped 26 / 641 bins on chromosome 10
Dropped 39 / 793 bins on chromosome 11
concurrent.futures.process._RemoteTraceback: 
"""
Traceback (most recent call last):
  File "/opt/conda/lib/python3.10/concurrent/futures/process.py", line 246, in _process_worker
    r = call_item.fn(*call_item.args, **call_item.kwargs)
  File "/opt/conda/lib/python3.10/concurrent/futures/process.py", line 205, in _process_chunk
    return [fn(*args) for args in chunk]
  File "/opt/conda/lib/python3.10/concurrent/futures/process.py", line 205, in <listcomp>
    return [fn(*args) for args in chunk]
  File "/opt/conda/lib/python3.10/site-packages/cnvlib/segmentation/__init__.py", line 126, in _ds
    return _do_segmentation(*args)
  File "/opt/conda/lib/python3.10/site-packages/cnvlib/segmentation/__init__.py", line 238, in _do_segmentation
    segarr = transfer_fields(segarr, cnarr)
  File "/opt/conda/lib/python3.10/site-packages/cnvlib/segmentation/__init__.py", line 347, in transfer_fields
    seg_gn = ",".join(subgenes)
TypeError: sequence item 3: expected str instance, float found
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/opt/conda/bin/cnvkit.py", line 8, in <module>
    sys.exit(main())
  File "/opt/conda/lib/python3.10/site-packages/cnvlib/cnvkit.py", line 10, in main
    args.func(args)
  File "/opt/conda/lib/python3.10/site-packages/cnvlib/commands.py", line 1022, in _cmd_segment
    results = segmentation.do_segmentation(
  File "/opt/conda/lib/python3.10/site-packages/cnvlib/segmentation/__init__.py", line 81, in do_segmentation
    rets = list(
  File "/opt/conda/lib/python3.10/concurrent/futures/process.py", line 575, in _chain_from_iterable_of_lists
    for element in iterable:
  File "/opt/conda/lib/python3.10/concurrent/futures/_base.py", line 621, in result_iterator
    yield _result_or_cancel(fs.pop())
  File "/opt/conda/lib/python3.10/concurrent/futures/_base.py", line 319, in _result_or_cancel
    return fut.result(timeout)
  File "/opt/conda/lib/python3.10/concurrent/futures/_base.py", line 458, in result
    return self.__get_result()
  File "/opt/conda/lib/python3.10/concurrent/futures/_base.py", line 403, in __get_result
    raise self._exception
TypeError: sequence item 3: expected str instance, float found

I tried to install CNVkit using both conda and docker (the output above is from a docker run) but I always get the same error. The head of the .cnr file looks like that:

chromosome	start	end	gene	log2	depth	gc	tx_length	weight
1	12010	13670	DDX11L1	0.92298	12.5	0.5912	632	0.339448
1	14696	24886	WASH7P	-0.101195	7.89855	0.5657	1380	0.445155
1	131025	134836	CICP27	0.109838	3.17419	0.5971	3812	0.230832
1	141474	173862	nan	0.344426	3.86831	0.4496	4860	0.323938
1	185217	195411	WASH9P	0.0415028	16.5354	0.5654	1397	0.24177
1	258568	259024	nan	-0.320253	12.6915	0.5077	457	0.25314
1	347982	348366	RPL23AP24	0.397249	1.81818	0.5039	385	0.236658
1	485026	485208	nan	-0.282081	61.7486	0.4044	183	0.23707
1	487101	489906	CICP7	0.216113	0.242229	0.6169	2477	0.249926

Any idea? Thank you in advance!