Closed biostatShao closed 2 days ago
When using Command Line Scripts magenpy_ld, I encounter different issues depending on the backend configuration.
If I use the default backend xarry, I get the error "BLAS : Program is Terminated. Because you tried to allocate too many memory regions."
If I switch the backend to plink1.9, I encounter the following traceback:
/home/zhshao/anaconda3/envs/py3/lib/python3.7/site-packages/scipy/sparse/_index.py:125: SparseEfficiencyWarning: Changing the sparsity structure of a csr_matrix is expensive. lil_matrix is more efficient.
self._set_arrayXarray(i, j, x)
Traceback (most recent call last):
File "/home/zhshao/anaconda3/envs/py3/bin/magenpy_ld", line 173, in
I am encountering these issues with both magenpy v0.0.12 and v0.0.11. How can I resolve this?
Hi Zhonghe,
The xarray
backend is not memory-efficient, so I don't recommend using it to compute very large LD matrices.
Regarding the error with plink1.9
, please upgrade to magenpy>0.1
. This issue has been resolved in the latest versions of the package.
Thanks! We're working on adding this feature as part of a new release of the
viprs
software. We will also be releasing LD matrices for 6 continental populations represented in the UK Biobank in the next couple of weeks.Do you mind opening a separate issue (here or under
viprs
) about the issues you're having with theshrinkage
estimator? Which versions of themagenpy
/viprs
are you using? Which data did you compute the LD matrix from? How did you go about runningviprs
? All of these details can help us improve the software.Thanks,
Shadi
Originally posted by @shz9 in https://github.com/shz9/magenpy/issues/10#issuecomment-2161174513