Error code in convering summary statistics

[dor25]

I wonder if you can offer any advice please in my error code in converting summary statistics. Package seems to read in the summary statistics fine. I wonder if you can offer help to unpick my error please if possible? Thank you kindly, Victoria

ERROR converting summary statistics:

Traceback (most recent call last):
File "/opt/mtag/mtag_munge.py", line 882, in munge_sumstats
check_median(dat.SIGNED_SUMSTAT, signed_sumstat_null, args.median_z_cutoff, sign_cname))
File "/opt/mtag/mtag_munge.py", line 522, in check_median
m = np.median(x)
File "/usr/local/lib/python2.7/dist-packages/numpy/lib/function_base.py", line 3497, in median
overwrite_input=overwrite_input)
File "/usr/local/lib/python2.7/dist-packages/numpy/lib/function_base.py", line 3405, in _ureduce
r = func(a, **kwargs)
File "/usr/local/lib/python2.7/dist-packages/numpy/lib/function_base.py", line 3556, in _median
return mean(part[indexer], axis=axis, out=out)
File "/usr/local/lib/python2.7/dist-packages/numpy/core/fromnumeric.py", line 3118, in mean
out=out, **kwargs)
File "/usr/local/lib/python2.7/dist-packages/numpy/core/_methods.py", line 87, in _mean
ret = ret / rcount
TypeError: unsupported operand type(s) for /: 'str' and 'int'

[JonJala]

Hmm, it looks like it's reading in the file but assigning a type of "string" to the signed sumstat column (Z or Beta). There is likely something off about the column (could be some extra whitespace or missing values or some extra, non-numeric characters or probably several other causes) that isn't enough to cause Pandas to balk, but enough that it thinks that it's not all numbers.