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.

[GMFranceschini]

Same error here, any idea how to fix it?

[Rubbert]

I suspect it is purely a size issue. Is your data also quite big? That probably means you'll have to save the data some other way (e.g. as .csv.gz or something) and build up your object piece-by-piece (I think that's what I ended up doing).

[GMFranceschini]

That makes perfect sense, also given the other issues reported. Yes it's big, it is the Tabula Muris complete object from cellXgene in my case. Thank you for your advice!