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bulik / ldsc

LD Score Regression (LDSC)
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Error converting summary statistics #104

Open gnarw opened 6 years ago

gnarw commented 6 years ago

I´m getting errors from munge_sumstats I have recently updated some of the python packages, but I´m using python 2.7 The log with the error is not helping me finding the issue. (Attached file). iss.txt

Any ideas ?

rkwalters commented 6 years ago

Hello, From previous of that error (here https://github.com/bulik/ldsc/issues/93 and here https://groups.google.com/d/msg/ldsc_users/9Mxw4vAB2l8/Muc_vtmYAwAJ) is appears to be caused by changes in pandas 0.21. The current solution is to revert pandas to e.g. version 0.20.1.

@tpoterba: Can we look at whether this is fixable to support pandas 0.21 without breaking backwards compatibility?

Cheers, Raymond

On Feb 13, 2018, at 6:32 AM, gnarw notifications@github.com wrote:

I´m getting errors from munge_sumstats I have recently updated some of the python packages, but I´m using python 2.7 The log with the error is not helping me finding the issue. (Attached file). iss.txt https://github.com/bulik/ldsc/files/1719701/iss.txt Any ideas ?

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tpoterba commented 6 years ago

I don't think this makes much sense, since it'll just break in the next version. I think the current plan is to release a conda environment with the known passing versions (which I think is pandas 0.17).

gnarw commented 6 years ago

Reverting to pandas 0.18.1 solved this issue. I had to revert to 0.18.1, else there were also problems when estimating the genetic correlation.