I encountered the following errors when running 'cnvkit.py target baits.bed --annotate refFlat.txt --split -o targets.bed'. I have no problem running 'cnvkit.py access' and 'guess_baits.py'. I installed CNVkit using by creating a conda environment as suggested. The python version is 3.9.18.
Detected file format: interval
Splitting large targets
cnvkit/lib/python3.9/site-packages/skgenome/combiners.py:53: FutureWarning: unique with argument that is not not a Series, Index, ExtensionArray, or np.ndarray is deprecated and will raise in a future version.
return sep.join(pd.unique(elems))
Traceback (most recent call last):
File "cnvkit/lib/python3.9/site-packages/pandas/core/groupby/groupby.py", line 1766, in apply
result = self._python_apply_general(f, self._selected_obj)
File "cnvkit/lib/python3.9/site-packages/pandas/core/groupby/groupby.py", line 1815, in _python_apply_general
values, mutated = self.grouper.apply_groupwise(f, data, self.axis)
File "cnvkit/lib/python3.9/site-packages/pandas/core/groupby/ops.py", line 905, in apply_groupwise
res = f(group)
File "cnvkit/lib/python3.9/site-packages/pandas/core/groupby/groupby.py", line 1754, in f
return func(g, *args, **kwargs)
File "cnvkit/lib/python3.9/site-packages/skgenome/merge.py", line 164, in _merge_overlapping
merged_rows = [
File "cnvkit/lib/python3.9/site-packages/skgenome/merge.py", line 165, in
_squash_tuples(row_group, combine)
File "cnvkit/lib/python3.9/site-packages/skgenome/merge.py", line 217, in _squash_tuples
newfields = {
File "cnvkit/lib/python3.9/site-packages/skgenome/merge.py", line 218, in
key: combiner([getattr(r, key) for r in rows])
File "cnvkit/lib/python3.9/site-packages/skgenome/combiners.py", line 53, in join_strings
return sep.join(pd.unique(elems))
TypeError: sequence item 0: expected str instance, numpy.float64 found
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "cnvkit/bin/cnvkit.py", line 10, in
sys.exit(main())
File "cnvkit/lib/python3.9/site-packages/cnvlib/cnvkit.py", line 10, in main
args.func(args)
File "cnvkit/lib/python3.9/site-packages/cnvlib/commands.py", line 389, in _cmd_target
regions = target.do_target(
File "cnvkit/lib/python3.9/site-packages/cnvlib/target.py", line 18, in do_target
tgt_arr = tgt_arr.subdivide(avg_size, 0)
File "cnvkit/lib/python3.9/site-packages/skgenome/gary.py", line 689, in subdivide
return self.as_dataframe(subdivide(self.data, avg_size, min_size, verbose))
File "cnvkit/lib/python3.9/site-packages/skgenome/subdivide.py", line 18, in subdivide
return pd.DataFrame.from_records(
File "cnvkit/lib/python3.9/site-packages/pandas/core/frame.py", line 2307, in from_records
first_row = next(data)
File "cnvkit/lib/python3.9/site-packages/skgenome/subdivide.py", line 41, in _split_targets
for row in merge(regions).itertuples(index=False):
File "cnvkit/lib/python3.9/site-packages/skgenome/merge.py", line 148, in merge
table.groupby(by=groupkey, as_index=False, group_keys=False, sort=False)
File "cnvkit/lib/python3.9/site-packages/pandas/core/groupby/groupby.py", line 1776, in apply
return self._python_apply_general(f, self._obj_with_exclusions)
File "cnvkit/lib/python3.9/site-packages/pandas/core/groupby/groupby.py", line 1815, in _python_apply_general
values, mutated = self.grouper.apply_groupwise(f, data, self.axis)
File "cnvkit/lib/python3.9/site-packages/pandas/core/groupby/ops.py", line 905, in apply_groupwise
res = f(group)
File "cnvkit/lib/python3.9/site-packages/pandas/core/groupby/groupby.py", line 1754, in f
return func(g, *args, **kwargs)
File "cnvkit/lib/python3.9/site-packages/skgenome/merge.py", line 164, in _merge_overlapping
merged_rows = [
File "cnvkit/lib/python3.9/site-packages/skgenome/merge.py", line 165, in
_squash_tuples(row_group, combine)
File "cnvkit/lib/python3.9/site-packages/skgenome/merge.py", line 217, in _squash_tuples
newfields = {
File "cnvkit/lib/python3.9/site-packages/skgenome/merge.py", line 218, in
key: combiner([getattr(r, key) for r in rows])
File "cnvkit/lib/python3.9/site-packages/skgenome/merge.py", line 218, in
key: combiner([getattr(r, key) for r in rows])
AttributeError: 'Pandas' object has no attribute 'chromosome'
Dear developer,
I encountered the following errors when running 'cnvkit.py target baits.bed --annotate refFlat.txt --split -o targets.bed'. I have no problem running 'cnvkit.py access' and 'guess_baits.py'. I installed CNVkit using by creating a conda environment as suggested. The python version is 3.9.18.
Detected file format: interval Splitting large targets cnvkit/lib/python3.9/site-packages/skgenome/combiners.py:53: FutureWarning: unique with argument that is not not a Series, Index, ExtensionArray, or np.ndarray is deprecated and will raise in a future version. return sep.join(pd.unique(elems)) Traceback (most recent call last): File "cnvkit/lib/python3.9/site-packages/pandas/core/groupby/groupby.py", line 1766, in apply result = self._python_apply_general(f, self._selected_obj) File "cnvkit/lib/python3.9/site-packages/pandas/core/groupby/groupby.py", line 1815, in _python_apply_general values, mutated = self.grouper.apply_groupwise(f, data, self.axis) File "cnvkit/lib/python3.9/site-packages/pandas/core/groupby/ops.py", line 905, in apply_groupwise res = f(group) File "cnvkit/lib/python3.9/site-packages/pandas/core/groupby/groupby.py", line 1754, in f return func(g, *args, **kwargs) File "cnvkit/lib/python3.9/site-packages/skgenome/merge.py", line 164, in _merge_overlapping merged_rows = [ File "cnvkit/lib/python3.9/site-packages/skgenome/merge.py", line 165, in
_squash_tuples(row_group, combine)
File "cnvkit/lib/python3.9/site-packages/skgenome/merge.py", line 217, in _squash_tuples
newfields = {
File "cnvkit/lib/python3.9/site-packages/skgenome/merge.py", line 218, in
key: combiner([getattr(r, key) for r in rows])
File "cnvkit/lib/python3.9/site-packages/skgenome/combiners.py", line 53, in join_strings
return sep.join(pd.unique(elems))
TypeError: sequence item 0: expected str instance, numpy.float64 found
During handling of the above exception, another exception occurred:
Traceback (most recent call last): File "cnvkit/bin/cnvkit.py", line 10, in
sys.exit(main())
File "cnvkit/lib/python3.9/site-packages/cnvlib/cnvkit.py", line 10, in main
args.func(args)
File "cnvkit/lib/python3.9/site-packages/cnvlib/commands.py", line 389, in _cmd_target
regions = target.do_target(
File "cnvkit/lib/python3.9/site-packages/cnvlib/target.py", line 18, in do_target
tgt_arr = tgt_arr.subdivide(avg_size, 0)
File "cnvkit/lib/python3.9/site-packages/skgenome/gary.py", line 689, in subdivide
return self.as_dataframe(subdivide(self.data, avg_size, min_size, verbose))
File "cnvkit/lib/python3.9/site-packages/skgenome/subdivide.py", line 18, in subdivide
return pd.DataFrame.from_records(
File "cnvkit/lib/python3.9/site-packages/pandas/core/frame.py", line 2307, in from_records
first_row = next(data)
File "cnvkit/lib/python3.9/site-packages/skgenome/subdivide.py", line 41, in _split_targets
for row in merge(regions).itertuples(index=False):
File "cnvkit/lib/python3.9/site-packages/skgenome/merge.py", line 148, in merge
table.groupby(by=groupkey, as_index=False, group_keys=False, sort=False)
File "cnvkit/lib/python3.9/site-packages/pandas/core/groupby/groupby.py", line 1776, in apply
return self._python_apply_general(f, self._obj_with_exclusions)
File "cnvkit/lib/python3.9/site-packages/pandas/core/groupby/groupby.py", line 1815, in _python_apply_general
values, mutated = self.grouper.apply_groupwise(f, data, self.axis)
File "cnvkit/lib/python3.9/site-packages/pandas/core/groupby/ops.py", line 905, in apply_groupwise
res = f(group)
File "cnvkit/lib/python3.9/site-packages/pandas/core/groupby/groupby.py", line 1754, in f
return func(g, *args, **kwargs)
File "cnvkit/lib/python3.9/site-packages/skgenome/merge.py", line 164, in _merge_overlapping
merged_rows = [
File "cnvkit/lib/python3.9/site-packages/skgenome/merge.py", line 165, in
_squash_tuples(row_group, combine)
File "cnvkit/lib/python3.9/site-packages/skgenome/merge.py", line 217, in _squash_tuples
newfields = {
File "cnvkit/lib/python3.9/site-packages/skgenome/merge.py", line 218, in
key: combiner([getattr(r, key) for r in rows])
File "cnvkit/lib/python3.9/site-packages/skgenome/merge.py", line 218, in
key: combiner([getattr(r, key) for r in rows])
AttributeError: 'Pandas' object has no attribute 'chromosome'