voila tsv error

[Yu Sun]

Hi there, 

I ran majiq-v3 without problem but encountered the following error when trying to run voila tsv on result from heterogen. I have the error message attached. Any help to resolve this would be greatly appreciated. 

Thank you!

Yu

[San Jewell]

Hello Yu,

As a first item, please note that python3.12 is the officially supported version for majiq release version 3.

I have tried running heterogen TSV on the currently released version of majiq/voila and I've not been able to reproduce this issue yet. However, please note that over the past few months, there have been a lot of bug fixed pushed out due to user feedback, so as a first step I'd recommend trying to reinstall/update your majiq/voila installation and see if that fixes the issue straightaway.

If not, I would ask for a list of commands you used to get to this point in the process, either redacted or sent to me directly, so that I can see if there may be an edge case which leads to the errors.

Let me know if you have a chance.

Thanks,

-San

[Yu Sun]

Thanks San,

Could you please tell me the version information for other dependencies? I'll try to reinstall majiq/voila.

Best,

Yu

[Yu Sun]

Hi San,

I reinstalled majiq and voila with python 3.12 but still got the same error when running voila. I attached all my commands and the error message. 

Thank you!

Best,

Yu

[Yu Sun]

I noticed that majiq-v3 build doesn't generate a sql file for me. It generates a folder called sg.zarr containing folders and files shown in the screenshot. Could this be the problem?

[San Jewell]

Hi Yu,

My mistake, I was actually getting confused between two identical threads on the board. I was able to reproduce the issue which was a problem with the --show-read-counts option. I have patched in a fix and the problem should be resolved. Please reinstall voila and try again when you have a moment. This should only require re-running the voila command, not the rest of the steps.

Thanks,

-San