KeyError: u"None of [Int64Index([-1, -2, -1, -2, -2, -1, -1, -1, -1, -1,\n

[jielab]

Hi, guys:

I saw quite some papers using the LDSC tool, so I am trying to learn how to use it.
The manual for installation seems quite simple, just a few lines.
The only place with a question mark is Anaconda. I am not sure if I should use Anaconda2 or Anaconda3. I tried both but got the same error. It seems that LDSC only works with Python2, correct?

Please see the attached log file. I was able to run munge_sumstats.py -h successfully, but I got error message when I use it to process an actual dataset.

Can someone please kindly help me to figure this out? I am using the Ubuntu Linux coming with Windows 10.

Thank you very much & Best regards,
Jie

Munge_sumstats.log

[armartin]

#185 fixed this issue for me.

[jdblischak]

The error message is due to a breaking change introduced in pandas 0.21.0 (changelog entry). If you're receiving this error, check the version of pandas you have installed.

Installing the dependencies via pip and requirements.txt or via conda and environment.yml will install pandas<0.21.0:

ldsc/requirements.txt

Line 6 in aa33296

pandas>=0.20,<0.21

ldsc/environment.yml

Line 12 in aa33296

- pandas==0.20

Using LDSC from commit 12e2687 (the version currently packaged in the bioconda recipe), I confirmed that munge_sumstats.py works with pandas 0.20.3, but with 0.21.0 I get the KeyError:

KeyError: '[-1 -1 -1 ... -1 -2 -2] not in index'

If you want to use a more recent version of pandas, pull from master to get the fix introduced in #185.