danielpodlesny / samestr

SameStr identifies shared strains between pairs of metagenomic samples based on the similarity of SNV profiles.
GNU Affero General Public License v3.0
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after installation, when runing samestr it says ´Illegal instruction (core dumped)´ #3

Closed huyue87 closed 2 years ago

huyue87 commented 2 years ago

Hello! After installed samestr and activated the env, when running samestr -v , samestr -h or samestr db, it said "Illegal instruction (core dumped) ".
I had the requried softwares installed on the server with maybe higher versions. both python2 and 3 were installed. Do you know what could be the problem? Is that mean the installation is not successful?

`$ pip install .
DEPRECATION: Python 2.7 reached the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 is no longer maintained. pip 21.0 will drop support for Python 2.7 in January 2021. More de tails about Python 2 support in pip, can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support
Processing /ceph/projects/038_Bactavia/5.SameStr/samestr
Building wheels for collected packages: samestr
Building wheel for samestr (setup.py) ... done
Created wheel for samestr: filename=samestr-2020.10-py2-none-any.whl size=92306 sha256=eefc1db0b6776dd3d64132ef3e4ffd4053a13ae039296049aaee3dd3afbc20c3
Stored in directory: /tmp/pip-ephem-wheel-cache-KJm7M3/wheels/00/32/f2/dfe4b0ccc92a5dff90ed86c51293b4c28edd198c0748c6ca7b
Successfully built samestr
Installing collected packages: samestr
Successfully installed samestr-2020.10

(samestr) [xxx@hitachi samestr]$ samestr -v
Illegal instruction (core dumped) `

danielpodlesny commented 2 years ago

Hi @huyue87,

It seems that you might be running into Illegal instruction (core dumped) due to the version of numpy within your environment (https://github.com/numpy/numpy/issues/18131).

Have you tried installing SameStr within conda as recommended in the installation instructions? By following the instructions your system should install all compatible software versions that are needed to get SameStr running.

Let me know if it works.

huyue87 commented 2 years ago

@danielpodlesny , Thanks! samestr works properly after upgrade the numpy version. I used conda to install samestr as you suggested.