TypeError: NDFrame._add_numeric_operations.<locals>.any() takes 1 positional argument but 2 were given

[kwonej0617]

Hi, Thank you for developing the useful tool.
It is my first time running Differr. My command line was as follows.

differr -a ${ko_bam} -b ${wt_bam} -r ${ref} -o differr.bed -f 2 --median-expr-threshold 0 --min-expr-threshold 0 -p 16

However, I got an error message. Could you please help me how to solve the error?

joblib.externals.loky.process_executor._RemoteTraceback:

Traceback (most recent call last):
File "/share/pkg/conda/differr_nanopore_drs/0.2/lib/python3.10/site-packages/joblib/externals/loky/process_executor.py", line 428, in _process_worker
r = call_item()
File "/share/pkg/conda/differr_nanopore_drs/0.2/lib/python3.10/site-packages/joblib/externals/loky/process_executor.py", line 275, in call
return self.fn(*self.args, **self.kwargs)
File "/share/pkg/conda/differr_nanopore_drs/0.2/lib/python3.10/site-packages/joblib/_parallel_backends.py", line 620, in call
return self.func(*args, **kwargs)
File "/share/pkg/conda/differr_nanopore_drs/0.2/lib/python3.10/site-packages/joblib/parallel.py", line 288, in call
return [func(*args, **kwargs)
File "/share/pkg/conda/differr_nanopore_drs/0.2/lib/python3.10/site-packages/joblib/parallel.py", line 288, in
return [func(*args, **kwargs)
File "/share/pkg/conda/differr_nanopore_drs/0.2/lib/python3.10/site-packages/differr-0.2-py3.10.egg/differr/main.py", line 65, in _parallel_differr
stats, mismatch_counts = test_significant_der_sites(counts, fdr_threshold, fasta)
File "/share/pkg/conda/differr_nanopore_drs/0.2/lib/python3.10/site-packages/differr-0.2-py3.10.egg/differr/statistics.py", line 33, in test_significant_der_sites
c = filter_empty_cols(c.unstack(-1))
File "/share/pkg/conda/differr_nanopore_drs/0.2/lib/python3.10/site-packages/differr-0.2-py3.10.egg/differr/statistics.py", line 22, in filter_empty_cols
c_t = c_t[c_t.any(1)]
TypeError: NDFrame._add_numeric_operations..any() takes 1 positional argument but 2 were given
"""

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

Traceback (most recent call last):
File "/share/pkg/conda/differr_nanopore_drs/0.2/bin/differr", line 33, in
sys.exit(load_entry_point('differr==0.2', 'console_scripts', 'differr')())
File "/share/pkg/conda/differr_nanopore_drs/0.2/lib/python3.10/site-packages/click/core.py", line 1130, in call
return self.main(*args, **kwargs)
File "/share/pkg/conda/differr_nanopore_drs/0.2/lib/python3.10/site-packages/click/core.py", line 1055, in main
rv = self.invoke(ctx)
File "/share/pkg/conda/differr_nanopore_drs/0.2/lib/python3.10/site-packages/click/core.py", line 1404, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/share/pkg/conda/differr_nanopore_drs/0.2/lib/python3.10/site-packages/click/core.py", line 760, in invoke
return __callback(*args, **kwargs)
File "/share/pkg/conda/differr_nanopore_drs/0.2/lib/python3.10/site-packages/differr-0.2-py3.10.egg/differr/main.py", line 170, in differr
File "/share/pkg/conda/differr_nanopore_drs/0.2/lib/python3.10/site-packages/differr-0.2-py3.10.egg/differr/main.py", line 101, in run_differr_analysis
File "/share/pkg/conda/differr_nanopore_drs/0.2/lib/python3.10/site-packages/joblib/parallel.py", line 1098, in call
self.retrieve()
File "/share/pkg/conda/differr_nanopore_drs/0.2/lib/python3.10/site-packages/joblib/parallel.py", line 975, in retrieve
self._output.extend(job.get(timeout=self.timeout))
File "/share/pkg/conda/differr_nanopore_drs/0.2/lib/python3.10/site-packages/joblib/_parallel_backends.py", line 567, in wrap_future_result
return future.result(timeout=timeout)
File "/share/pkg/conda/differr_nanopore_drs/0.2/lib/python3.10/concurrent/futures/_base.py", line 458, in result
return self.__get_result()
File "/share/pkg/conda/differr_nanopore_drs/0.2/lib/python3.10/concurrent/futures/_base.py", line 403, in __get_result
raise self._exception
TypeError: NDFrame._add_numeric_operations..any() takes 1 positional argument but 2 were given

Thank you so much!

[Madhurananda]

Hi @kwonej0617

Change line 22 in statistics.py
from c_t = c_t[c_t.any(1)] to:
c_t = c_t[c_t.any(axis=1)]

Then:
python setup.py install

This issue should be solved.

[kwonej0617]

Thank you for your help! I will try it.

[kwonej0617]

Hi, I modified the script in statistics.py and rerun setup.py to reinstall as you suggested.
Then, I run the script again, but it printed out the following message in the error log file.

PLEASE NOTE: the differr_nanopore_drs/0.2 module is loading a conda environment
in an experimental way. If you encounter problems please report them to
[email protected]. This installation has been modified per the recommendation at
https://github.com/bartongroup/differr_nanopore_DRS/issues/5 

It has been running for a day, but nothing was generated in the output directory. Should I wait for a few more hours/days to get the output? I would appreciate it if you could give me any advice on this. Thank you!

[Madhurananda]

Hi @kwonej0617

I am also having the same issue and I need to investigate deeper.
I will share my success here if I can find any.

Also in the meantime, if you can get something interesting, please also share it here for everyone's benefit.

[kwonej0617]

Hi, @Madhurananda, @mparker2

I just wanted to share another error message I got during the process.
/share/pkg/conda/differr_nanopore_drs/0.2/lib/python3.10/site-packages/differr-0.2-py3.10.egg/differr/output.py:37: RuntimeWarning: divide by zero encountered in log10

Though I got the messages, I just kept it running, and it generated an output file.
However, my result looks weird. It doesn't have the score value, G statistic for the homogeneity test of mutant replicates, -log10 P value for the homogeneity test of mutant replicates, G statistic for the homogeneity test of wild type replicates, -log10 P value for the homogeneity test of wild type replicates.

ENST00000618786 249     250     DER_site        -0      +       -0.63   0.00    -0.00   -0.00   nan     nan     nan     nan
ENST00000618786 252     253     DER_site        -0      +       -2.49   0.01    0.03    -0.00   nan     nan     nan     nan
ENST00000618786 258     259     DER_site        -0      +       0.28    0.00    -0.00   -0.00   nan     nan     nan     nan
ENST00000618786 256     257     DER_site        -0      +       0.93    0.00    -0.00   -0.00   nan     nan     nan     nan
ENST00000618786 257     258     DER_site        -0      +       1.83    0.18    0.17    -0.00   nan     nan     nan     nan
ENST00000618786 259     260     DER_site        -0      +       0.28    3.65    0.79    -0.00   nan     nan     nan     nan
ENST00000618786 260     261     DER_site        -0      +       -3.39   3.80    0.83    -0.00   nan     nan     nan     nan
ENST00000618786 268     269     DER_site        -0      +       0.93    0.00    -0.00   -0.00   nan     nan     nan     nan

Please let me know if you solve the problem. Thank you so much!

[peterthorpe5]

@kwonej0617 Im not part of the team that made this ... I am here for another error. I would say that the version of python you are using may be too new. 3.10 is a lot newer than when the code was written. This may or may not be the issue. I hope that help.

[peterthorpe5]

I got this error "/share/pkg/conda/differr_nanopore_drs/0.2/lib/python3.10/site-packages/differr-0.2-py3.10.egg/differr/output.py:37: RuntimeWarning: divide by zero encountered in log10" - but more sensible output using python 3.6