Issue running Epinano_Variants.py

[cednotsed]

With reference to a previously closed issue, I am facing the same problem running Epinano_Variants.

Process Process-2:
Traceback (most recent call last):
  File "/home/cedrict/miniconda3/lib/python3.6/multiprocessing/process.py", line 258, in _bootstrap
    self.run()
  File "/home/cedrict/miniconda3/lib/python3.6/multiprocessing/process.py", line 93, 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

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.

[Huanle]

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!

[cednotsed]

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.

[Huanle]

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

[cednotsed]

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

[Huanle]

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.

[Huanle]

Hi @cednotsed , Can you try with the latest Epinano_Variants.py and let me know whether it works?