Disentangling failed: No module named scipy

[SSmith-NUIG]

get_org_private.log.txt
Hi,
GetOrganelle seems unable to import scipy for the disentangling stage.

I'm running it on an anaconda environment with python 3.6.
If I run python in the terminal and type import scipy it works no problem.
If I create a testing python script which imports scipy it also works with no problems.

From the log output:
PYTHON LIBS: GetOrganelleLib 1.7.5; numpy 1.18.5; sympy 1.5.1; scipy 1.5.2

[Kinggerm]

Please ALWAYS attach the get_org.log.txt file if applicable

[SSmith-NUIG]

Please ALWAYS attach the get_org.log.txt file if applicable

Attached it to the OP now.

[Kinggerm]

Thanks!
Could you please resume the run with "--verbose --continue" attached and post the new log file here?

[SSmith-NUIG]

get_org_private_continue.log.txt

Thanks! Could you please resume the run with "--verbose --continue" attached and post the new log file here?

Will do tomorrow once I have access to the HPC again. I'll edit this post with the output

[Kinggerm]

Thanks for the feedback.
It still seems to be a scipy importing error because no other code blocks will trigger this error.

Could you please try following command inside the python of your HPC:

from scipy import stats, inf, log

[SSmith-NUIG]

Thanks for the feedback. It still seems to be a scipy importing error because no other code blocks will trigger this error.

Could you please try following command inside the python of your HPC:

from scipy import stats, inf, log

Thanks, that did the trick. My environment was missing some Mkl libraries.

[Kinggerm]

Good to know.

And thanks again. I have modified the associated code blocks, reporting from scipy import stats, inf, log error instead of No module named scipy.

[o-william-white]

Just to add, I got the same error with the example data but it was fixed by downgrading scipy from 1.12 to 1.11.3.

[JianjunJin]

@o-william-white Thanks a lot! It seems that scipy 1.12 does not have inf and log, which can be replaced with np.inf and np.log.

BTW, in the next big release, GetOrganelle uses gekko instead of scipy.

[JianjunJin]

Before the formal release of GetOrganelle 1.8.0, I just added some fixes to GetOrganelle 1.7.7.1, including compatibility with scipy 1.2. GetOrganelle 1.7.7.1 is now available in bioconda.

[o-william-white]

Thanks @Kinggerm