Closed saulvegasauceda closed 1 year ago
Hi @saulvegasauceda
Thanks for giving {zellkonverter} a go. I think what you might be interrupting is the creation of the {basilisk} Python environment. What happens if you just let it run? Does it finish eventually or just hang forever?
I've let it run for 11 hours, it did not finish. I think it's safe to assume it would have stalled indefinitely.
Usually the creation of the basilisk environment would be accompanied by a lot of noise and thunder from Conda. I don't see any of this in the stdout above; and besides, if this was interrupted, subsequent calls should not work.
I assume that the environment was already provisioned in the first call above. Suggest debug()
ing a relevant function and stepping through to see where the stall is occurring.
Thank you @LTLA @lazappi for responding!
It remains stalled until I interrupt it.
debug(writeH5AD(rna_data, h5_rna, verbose=TRUE))
ℹ Using anndata version 0.8.0
^C
Not sure what's causing this behavior but using the R.utils library function withTimeout()
bandaged the issue.
Here's what I did:
withTimeout({readH5AD(input_file, verbose = TRUE)}, timeout=120, onTimeout="silent")
rna_sce <- readH5AD(input_file, verbose = TRUE)
I think you need to use debug()
slightly differently. If you do:
debug(zellkonverter::readH5AD)
zellkonverter::readH5AD(input_file, verbose = TRUE)
That should open the debugging browser. Then you can step through the function line by line and see which line is getting stuck. Depending on where it is debug(zellkonverter::AnnData2SCE)
might be more useful.
Do you have this issue on another machine and/or with different input files?
Closing this issue as I hope it has been resolved in recent releases.
Hello, I ran into this weird behavior when running
readH5AD
. For some reason, every first invocation ofreadH5AD
stalls up to the point of displaying the anndata version. However, if I interrupt this call then the following invocations ofreadH5AD
work as expected. Is there a way I could get this to work without the Keyboard Interruption?I am trying to run this call for 72 h5 files so ideally I would want this to be done without any user interaction.
Thanks, Saul
Example:
R session info: