running velorama

[daniel-spies]

Hi,

I've encountered several issues running velorama

1. precomputed pseudotime has to be saved in adata.obs['pseudotime'] though scVelo saves it either as dpt_pseudotime or velocity_pseudotime
2. the ray.init in run.py kills the process on a cluster as it tries to spawn as many processes as cpus are detected, if this differs from the number that were requested the worker process is killed, so here an additional parameter to define the number of cores to be used would be helpful . the same is true for the memory if the user supplies less than 10GB, this should be anothe parameter
3. when creating is_target and is_reg as suggested by the code in the github repo, it's an adata.var entry of the same length with logical values, in the code it's simply taking the shape, so the status message prints the dimension of adata.var and not the actual number of regulators and targets. hope this is just the print statement and not affecting downstream analysis. For the proper print statement rather use X.sum() and Y.sum()

best
Daniel

[rs239]

Hi Daniel, Thanks for these bug reports! We'll work on fixing them and share an update shortly.

…

-r

On Tue, Mar 14, 2023, 12:47 PM daniel-spies ***@***.***> wrote: Hi, I've encountered several issues running velorama 1. precomputed pseudotime has to be saved in adata.obs['pseudotime'] though scVelo saves it either as dpt_pseudotime or velocity_pseudotime 2. the ray.init in run.py kills the process on a cluster as it tries to spawn as many processes as cpus are detected, if this differs from the number that were requested the worker process is killed, so here an additional parameter to define the number of cores to be used would be helpful . the same is true for the memory if the user supplies less than 10GB, this should be anothe parameter 3. when creating is_target and is_reg as suggested by the code in the github repo, it's an adata.var entry of the same length with logical values, in the code it's simply taking the shape, so the status message prints the dimension of adata.var and not the actual number of regulators and targets. hope this is just the print statement and not affecting downstream analysis. For the proper print statement rather use X.sum() and Y.sum() best Daniel — Reply to this email directly, view it on GitHub <#2>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABSO3WPXB55K53J3YZJ7WJTW4COIXANCNFSM6AAAAAAV2WLMCI> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[daniel-spies]

sorry, the X.sum() doesn't make sense as the array will be created properly, the issue is if -rt 1 (reg_target) argument is not used all the genes will be considered targets and regulators.

this is insufficiently explained in the documentation ..