saveh5 running for very long time

[mehtar1]

Hi! I'm new to running Lamian, but I'm currently trying to use the saveh5 function to save expression data in the hdf5 file format. My dataset is somewhat large (40k cells, 36k genes), yet I submitted a job to save the files and it has been running for 18 hours. Is there a reason saving in this file format is taking so long? Do you have any suggestions for reducing the runtime, or is this an issue with the function? Thanks!

[yimwy]

Hi, same issue here with dataset comprised of ~5k metacells and 20k genes. Is there a solution?

[Winnie09]

Hi,

Thanks for your interest! saveh5 is taking a long time, and I haven't got a better solution, unfortunately. I marked this question to see if anyone else can help.

Best,
Wenpin