Python, how to handle the “ValueError: unsupported pickle protocol: 4” error?

Question

I'm new to Python. I've to run this TargetFinder script ("Custom Analyses") .

I installed all the required python packages, and copied the code into a script I named main.py , and ran it. I got this error:

[davide@laptop]$ python main.py 
Traceback (most recent call last):
  File "main.py", line 8, in <module>
    training_df = pd.read_hdf('./paper/targetfinder/K562/output-epw/training.h5', 'training').set_index(['enhancer_name', 'promoter_name'])
  File "/usr/lib64/python2.7/site-packages/pandas/io/pytables.py", line 330, in read_hdf
    return store.select(key, auto_close=auto_close, **kwargs)
  File "/usr/lib64/python2.7/site-packages/pandas/io/pytables.py", line 680, in select
    return it.get_result()
  File "/usr/lib64/python2.7/site-packages/pandas/io/pytables.py", line 1364, in get_result
    results = self.func(self.start, self.stop, where)
  File "/usr/lib64/python2.7/site-packages/pandas/io/pytables.py", line 673, in func
    columns=columns, **kwargs)
  File "/usr/lib64/python2.7/site-packages/pandas/io/pytables.py", line 2786, in read
    values = self.read_array('block%d_values' % i)
  File "/usr/lib64/python2.7/site-packages/pandas/io/pytables.py", line 2327, in read_array
    data = node[:]
  File "/usr/lib64/python2.7/site-packages/tables/vlarray.py", line 677, in __getitem__
    return self.read(start, stop, step)
  File "/usr/lib64/python2.7/site-packages/tables/vlarray.py", line 817, in read
    outlistarr = [atom.fromarray(arr) for arr in listarr]
  File "/usr/lib64/python2.7/site-packages/tables/atom.py", line 1211, in fromarray
    return cPickle.loads(array.tostring())
ValueError: unsupported pickle protocol: 4

I've no idea about what this pickle protocol means, and also my colleagues know nothing about it.

How can I solve this problem?

I'm using Python 2.7.5 on a CentOS Linux release 7.2.1511 (Core) operating system

Answer 1

The Pickle protocol is basically the file format. From the documentation , The higher the protocol used, the more recent the version of Python needed to read the pickle produced. ... Pickle protocol version 4 was added in Python 3.4 , your python version (2.7.5) does not support this.

Either upgrade to Python 3.4 or later (current is 3.5) or create the pickle using a lower protocol (2) in the third parameter to pickle.dump() .

Answer 2

This sometimes happens due to incorrect data in the redis database. Try it:

sudo redis-cli flushall

Answer 3

这是一个python版本问题，将其升级到最新的python版本并尝试。