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Disentangling failed: No module named scipy #132
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Please ALWAYS attach the |
Attached it to the OP now. |
Thanks! |
get_org_private_continue.log.txt
Will do tomorrow once I have access to the HPC again. I'll edit this post with the output |
Thanks for the feedback. Could you please try following command inside the python of your HPC:
|
Thanks, that did the trick. My environment was missing some Mkl libraries. |
Good to know. And thanks again. I have modified the associated code blocks, reporting |
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. |
@o-william-white Thanks a lot! It seems that BTW, in the next big release, GetOrganelle uses |
1. fix a import bug of 'from scipy import stat, log, inf' issue (issue #132 #315) 2. fix a ZeroDivisionError bug when the estimated coverage is 0 (issue #311) 3. Disentangling failed -> Disentangling unsuccessful to avoid panic (issue #308) 4. fix a bug in parsing options when '-F anonym' is used (issue #319) 5. have max_multiplicity passed to no-slim case 6. minor adjustment
Before the formal release of |
Thanks @Kinggerm |
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
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