Issue running MACS3

Question

[williamtmills]

I am having issues running MACS3. I installed MACS3 using:

wget https://github.com/macs3-project/MACS/archive/refs/tags/v3.0.0a6.tar.gz
tar -xf v3.0.0a6.tar.gz
chmod a+rwx MACS-3.0.0a6/bin/macs3

It appears to be installed correctly because the following code generates the predictd help window:

MACS-3.0.0a6/bin/macs3 predictd --help

However, when I try running the actual code I get the following error:

MACS-3.0.0a6/bin/macs3 predictd -i input.bam

Traceback (most recent call last):
  File "MACS-3.0.0a6/bin/macs3", line 727, in <module>
    main()
  File "MACS-3.0.0a6/bin/macs3", line 91, in main
    from MACS3.Commands.predictd_cmd import run
  File "/home/william/.local/lib/python3.8/site-packages/MACS3/Commands/predictd_cmd.py", line 22, in <module>
    from MACS3.Utilities.OptValidator import opt_validate_predictd
  File "/home/william/.local/lib/python3.8/site-packages/MACS3/Utilities/OptValidator.py", line 24, in <module>
    from MACS3.IO.Parser import BEDParser, ELANDResultParser, ELANDMultiParser, \
  File "MACS3/IO/Parser.pyx", line 1, in init MACS3.IO.Parser
ValueError: numpy.ndarray size changed, may indicate binary incompatibility. Expected 88 from C header, got 80 from PyObject

I can't make much sense of the error message. Any ideas about what is going wrong?

Thanks in advance for any help!

[ATpoint]

https://stackoverflow.com/questions/66060487/valueerror-numpy-ndarray-size-changed-may-indicate-binary-incompatibility-exp

Answer 1

[Sebastian]

I had the same problem as you. I had to downgrade python and numpy. I tried something like the minimum versions, which are written here: https://github.com/macs3-project/MACS/blob/master/docs/INSTALL.md. Like python 3.6, numpy 1.17, cython 0.29, and then magic happened and it runs on my PC. ;)

[ATpoint]

...or go easy and install with a package manager like conda which takes care of all that internally...