Closed grimwoo closed 4 years ago
Hi,
I am also getting this error.
Traceback (most recent call last):
File "/data/user/lucy/py36-v1/conda-install/envs/pyscenic/bin/pyscenic", line 8, in <module>
sys.exit(main())
File "/data/user/lucy/py36-v1/conda-install/envs/pyscenic/lib/python3.8/site-packages/pyscenic/cli/pyscenic.py", line 420, in main
args.func(args)
File "/data/user/lucy/py36-v1/conda-install/envs/pyscenic/lib/python3.8/site-packages/pyscenic/cli/pyscenic.py", line 159, in prune_targets_command
df_motifs = calc_func(dbs, modules, motif_annotations_fname,
File "/data/user/lucy/py36-v1/conda-install/envs/pyscenic/lib/python3.8/site-packages/pyscenic/prune.py", line 349, in prune2df
return _distributed_calc(rnkdbs, modules, motif_annotations_fname, transformation_func, aggregation_func,
File "/data/user/lucy/py36-v1/conda-install/envs/pyscenic/lib/python3.8/site-packages/pyscenic/prune.py", line 300, in _distributed_calc
return create_graph().compute(scheduler='processes', num_workers=num_workers if num_workers else cpu_count())
File "/data/user/lucy/py36-v1/conda-install/envs/pyscenic/lib/python3.8/site-packages/dask/base.py", line 166, in compute
(result,) = compute(self, traverse=False, **kwargs)
File "/data/user/lucy/py36-v1/conda-install/envs/pyscenic/lib/python3.8/site-packages/dask/base.py", line 444, in compute
results = schedule(dsk, keys, **kwargs)
File "/data/user/lucy/py36-v1/conda-install/envs/pyscenic/lib/python3.8/site-packages/dask/multiprocessing.py", line 208, in get
result = get_async(
File "/data/user/lucy/py36-v1/conda-install/envs/pyscenic/lib/python3.8/site-packages/dask/local.py", line 486, in get_async
raise_exception(exc, tb)
File "/data/user/lucy/py36-v1/conda-install/envs/pyscenic/lib/python3.8/site-packages/dask/local.py", line 316, in reraise
raise exc
File "/data/user/lucy/py36-v1/conda-install/envs/pyscenic/lib/python3.8/site-packages/dask/local.py", line 222, in execute_task
result = _execute_task(task, data)
File "/data/user/lucy/py36-v1/conda-install/envs/pyscenic/lib/python3.8/site-packages/dask/core.py", line 121, in _execute_task
return func(*(_execute_task(a, cache) for a in args))
File "/data/user/lucy/py36-v1/conda-install/envs/pyscenic/lib/python3.8/site-packages/dask/dataframe/utils.py", line 655, in check_meta
check_matching_columns(meta, x)
File "/data/user/lucy/py36-v1/conda-install/envs/pyscenic/lib/python3.8/site-packages/dask/dataframe/utils.py", line 680, in check_matching_columns
raise ValueError(
ValueError: The columns in the computed data do not match the columns in the provided metadata
Order of columns does not match
Was there a recommended solution?
Best, Lucy
Hi @grimwoo , @lc822 , sorry for not replying to this earlier. This is a common issue with Dask versions. You can find suggestions to fix this in #163
Hi,
I am also getting this error.
Traceback (most recent call last): File "/data/user/lucy/py36-v1/conda-install/envs/pyscenic/bin/pyscenic", line 8, in <module> sys.exit(main()) File "/data/user/lucy/py36-v1/conda-install/envs/pyscenic/lib/python3.8/site-packages/pyscenic/cli/pyscenic.py", line 420, in main args.func(args) File "/data/user/lucy/py36-v1/conda-install/envs/pyscenic/lib/python3.8/site-packages/pyscenic/cli/pyscenic.py", line 159, in prune_targets_command df_motifs = calc_func(dbs, modules, motif_annotations_fname, File "/data/user/lucy/py36-v1/conda-install/envs/pyscenic/lib/python3.8/site-packages/pyscenic/prune.py", line 349, in prune2df return _distributed_calc(rnkdbs, modules, motif_annotations_fname, transformation_func, aggregation_func, File "/data/user/lucy/py36-v1/conda-install/envs/pyscenic/lib/python3.8/site-packages/pyscenic/prune.py", line 300, in _distributed_calc return create_graph().compute(scheduler='processes', num_workers=num_workers if num_workers else cpu_count()) File "/data/user/lucy/py36-v1/conda-install/envs/pyscenic/lib/python3.8/site-packages/dask/base.py", line 166, in compute (result,) = compute(self, traverse=False, **kwargs) File "/data/user/lucy/py36-v1/conda-install/envs/pyscenic/lib/python3.8/site-packages/dask/base.py", line 444, in compute results = schedule(dsk, keys, **kwargs) File "/data/user/lucy/py36-v1/conda-install/envs/pyscenic/lib/python3.8/site-packages/dask/multiprocessing.py", line 208, in get result = get_async( File "/data/user/lucy/py36-v1/conda-install/envs/pyscenic/lib/python3.8/site-packages/dask/local.py", line 486, in get_async raise_exception(exc, tb) File "/data/user/lucy/py36-v1/conda-install/envs/pyscenic/lib/python3.8/site-packages/dask/local.py", line 316, in reraise raise exc File "/data/user/lucy/py36-v1/conda-install/envs/pyscenic/lib/python3.8/site-packages/dask/local.py", line 222, in execute_task result = _execute_task(task, data) File "/data/user/lucy/py36-v1/conda-install/envs/pyscenic/lib/python3.8/site-packages/dask/core.py", line 121, in _execute_task return func(*(_execute_task(a, cache) for a in args)) File "/data/user/lucy/py36-v1/conda-install/envs/pyscenic/lib/python3.8/site-packages/dask/dataframe/utils.py", line 655, in check_meta check_matching_columns(meta, x) File "/data/user/lucy/py36-v1/conda-install/envs/pyscenic/lib/python3.8/site-packages/dask/dataframe/utils.py", line 680, in check_matching_columns raise ValueError( ValueError: The columns in the computed data do not match the columns in the provided metadata Order of columns does not match
Was there a recommended solution?
Best, Lucy
Same problem here +1 👍
the package version is:
scanpy==1.4.4.post1 anndata==0.6.22.post1 umap==0.4.3 numpy==1.17.4 scipy==1.4.1 pandas==0.25.3 scikit-learn==0.23.1 statsmodels==0.11.1 pyscenic==0.10.0 dask=='2.17.2' distributed==2.11.0 pandas=='0.25.3'
I have try pip install dask==1.0.0 distributed'>=1.21.6,<2.0.0'
as the #163 said. but it doesn't work for me.
Then,I try the lastest version and the old version of pandas,just get the same error:
2020-06-04 11:25:13,096 - pyscenic.cli.pyscenic - INFO - Loading databases.
2020-06-04 11:25:13,096 - pyscenic.cli.pyscenic - INFO - Calculating regulons.
[ ] | 0% Completed | 13.7s
(omit)
File "/home/miniconda3/envs/ScCancer/lib/python3.8/site-packages/dask/dataframe/utils.py", line 680, in check_matching_columns
raise ValueError(
ValueError: The columns in the computed data do not match the columns in the provided metadata
Order of columns does not match
2020-06-04 11:26:18,390 - pyscenic.transform - WARNING - Less than 80% of the genes in Regulon for ZNF486 could be mapped to hg19-tss-centered-10kb-10species.mc9nr. Skipping this module.
2020-06-04 11:26:20,011 - pyscenic.transform - WARNING - Less than 80% of the genes in Regulon for ZNF492 could be mapped to hg19-tss-centered-10kb-10species.mc9nr. Skipping this module.
Is my Python version too new?
When I run
, it always gives me error.
As I read from a previous issue, this may be due to the module "dask". However, even though I tried half of historical versions of "dask", I still get the error information.
Error information with latest "dask" version is as following:
when I install lower version of "dask", the error would be like this (only sometimes, it could show "from dask ...."):