Jonathan Jala

The missing parentheses error is because you were trying to run with Python 3 initially, though mtag is written in Python 2 (where print is a statement and not a...

That looks right, I think (though you need a space between \"argparse\" and \"bitarray\"). I believe you can also [use](https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#creating-an-environment-from-an-environment-yml-file) the environment.yml file that comes with mtag.

You should be able to use the \"--ld_ref_panel\" flag to do that (see \"mtag.py -h\" for a full list of flags and options)

It needs to be split by chromosome, much like the panel included in MTAG. (The help message for the flag: "Specify folder of the ld reference panel **(split by chromosome)**...

I'll have to let someone else comment on whether the method is applicable in the way you're asking, but in terms of the wiki page link, it's right here off...

That error will be thrown when trying to use the beta-se option (there are bugs in that code we haven't been able to track down), so if you refrain from...

Hi, Anuj - Just wanted to confirm that you see "Performing grid search using 3 cores" in the log file? The joblib module handles the job/core allocation, and the number...

Hi, Anuj - Hmm, from what I understand, the steps before the grid search should generally not be too time-consuming (but apparently that's not the case, at least here). What...

It looks like this could be related to [issue #19](https://github.com/JonJala/mtag/issues/19)? Do you have P values that are very small?

You sure it's just 117? There is a line in your output \"2021/09/07/02:36:52 PM WARNING: 65759 SNPs had P outside of (0,1]. The P column may be mislabeled\"