Error when running test data

[stanislasmorand]

Dear Xie, I received an error message when I tried to run the test. I manually installed ISEScan and dependencies: numpy-1.19.2 scipy-1.5.2 fastcluster-1.1.26 FragGeneScan1.30 HMMER-3.3.1 BLAST 2.8.1 biopython-1.78 I also compiled the SSW library shipped with ISEScan as followed:

 cd /home/morands/ISESCAN/ISESSCAN-master/ssw201507
 gcc -Wall -O3 -pipe -fPIC -shared -rdynamic -o libssw.so ssw.c ssw.h
 cp libssw.so ../
 export LD_LIBRARY_PATH=/home/morands/ISESCAN/ISESSCAN-master:$LD_LIBRARY_PATH

I updated the constants.py file with appropriate path for the different variables.

Here is the message I received when running the command : python3 isescan.py NC_012624.fna proteome hmm --nthread 2

Traceback (most recent call last):
  File "/home/morands/LIBRARIES/numpy-1.19.2/numpy/__init__.py", line 124, in <module>
    from numpy.__config__ import show as show_config
ModuleNotFoundError: No module named 'numpy.__config__'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "isescan.py", line 10, in <module>
    import isPredict
  File "/home/morands/ISESCAN/ISEScan-master/isPredict.py", line 15, in <module>
    import pred
  File "/home/morands/ISESCAN/ISEScan-master/pred.py", line 14, in <module>
    import scipy.spatial.distance
  File "/home/morands/LIBRARIES/scipy-1.5.2/scipy/__init__.py", line 61, in <module>
    from numpy import show_config as show_numpy_config
  File "/home/morands/LIBRARIES/numpy-1.19.2/numpy/__init__.py", line 129, in <module>
    raise ImportError(msg)
ImportError: Error importing numpy: you should not try to import numpy from
        its source directory; please exit the numpy source tree, and relaunch
        your python interpreter from there.

Do you have an idea why there is an issue with the import of numpy? Thanks in advance for your precious help & time. Kindest regards. Stan

[xiezhq]

Hi Stan,

I don't have idea about this issue with the import of numpy. Based on the error report, it seems something wrong with your python3 environment and/or your numpy install. How did you install numpy and where is it installed on your machine?

Xie

[stanislasmorand]

Dear Xie, I corrected my $PYTHONPATH environment variable w/ correct export syntaxe. The test passed w/o error. Thanks again for your prompt reply. Stan