Closed cednotsed closed 4 years ago
Hi @cednotsed , Did you get any output(s)?
Can you list the pkgs you've installed?
pip list
I am trying to make containier. It should help people avoid some troubles.
Thanks!
Package Version
dask 2.28.0
fsspec 0.8.3
locket 0.2.0
numpy 1.19.2
pandas 0.25.1
partd 1.1.0
pip 18.1
pysam 0.16.0.1
python-dateutil 2.8.1
pytz 2020.1
PyYAML 5.3.1
setuptools 40.6.2
six 1.15.0
toolz 0.11.1
I did not get any output except an empty tmp directory.
Hi @cednotsed ,
While i am still tracking down into the details of this error, can you please try commands below and let me know whether it works?
python3.8 -m venv epinano12_py38 # [py38 can avoid issues associated with process communication via pickled data](https://github.com/enovoa/EpiNano/issues/59#issuecomment-699889046)
source epinano12_py38/bin/activate
pip install pandas
pip install dask==2.5.2
python -m pip install "dask[dataframe]"
pip install pysam
Package Version
cloudpickle 1.6.0
dask 2.5.2
fsspec 0.8.3
locket 0.2.0
numpy 1.19.2
pandas 1.1.2
partd 1.1.0
pip 19.2.3
pysam 0.16.0.1
python-dateutil 2.8.1
pytz 2020.1
setuptools 41.2.0
six 1.15.0
toolz 0.11.1
/hgst8TB/csctan/RNA_modifications/epinano12_py38/lib/python3.8/site-packages/dask/dataframe/utils.py:14: FutureWarning: pandas.util.testing is deprecated. Use the functions in the public API at pandas.testing instead. import pandas.util.testing as tm data/epinano_rna/raw_files/nomod_rep1/nomod_rep1.tmp_splitted already exists, will overwrite it Process Process-2: Traceback (most recent call last): File "/home/cedrict/miniconda3/envs/py3.8.3/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap self.run() File "/home/cedrict/miniconda3/envs/py3.8.3/lib/python3.8/multiprocessing/process.py", line 108, in run self._target(*self._args, **self._kwargs) File "/hgst8TB/csctan/EpiNano/epinano_modules.py", line 187, in split_tsv_for_per_site_var_freq head = next(tsv) StopIteration
Hi @cednotsed ,
Did you get any output? Do you mind sharing with me some of your input data, like a bam and reference sequences? Thanks.
Hi @cednotsed , Can you try with the latest Epinano_Variants.py and let me know whether it works?
With reference to a previously closed issue, I am facing the same problem running Epinano_Variants.
However, like @eliah-o, I had no luck getting the script to work despite trying out the python virtual environment you suggested nor with downgrading pandas to 0.24.2.
Please advise. Thanks.