negative length vectors are not allowed : Error when converting anndata to seurat

[bapoorva]

Hi,

I've used sceasy before with no issues. But this time, i tried to convert an h5ad file to a seurat object and got this error

Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 't': negative length vectors are not allowed

This is my code

library(sceasy)
library(reticulate)
use_python('/Users/bapoorva/miniconda3/bin/python3')
loompy <- reticulate::import('loompy')

sceasy::convertFormat("~/HLCA/local.h5ad", from="anndata", to="seurat",
                      outFile='HLCA_humanref.RDS')

I downloaded the h5ad from this link. It is the human reference file from the Human Lung Cell Atlas (HLCA)

Any ideas on how to resolve this ?

Thanks

[AlexandrePelletier]

I got the same error, anyone have been able to fix it ?

[Rubbert]

Same here. I wonder if it could be a memory/data size issue, I imagine the HLCA is quite large, and my test data is also ~600K cells.