Dear all,

I am experiencing an unusual error when trying to run any kind of partitioned heritability analysis. I believe this is a bug related to the _splitp function in sumstats.py. The error occurs with the most recent version of LDSC, but not - for instance - with version 1.0.0. Note that the error does not occur when calculating univariate LD scores, calculating heritability (not partitioned) or calculating correlations.

Example of error when running the partitioned heritability analysis with continuous annotations according to the wiki tutorial:

python /LDSC/ldsc/ldsc.py --h2 BMI.sumstats.gz --ref-ld-chr 1000G_Phase3_baselineLD_ldscores/baselineLD. --frqfile-chr 1000G_Phase3_frq/1000G.EUR.QC. --w-ld-chr 1000G_Phase3_weights_hm3_no_MHC/weights.hm3_noMHC. --overlap-annot --print-coefficients --print-delete-vals --out BMI.baselineLD

• LD Score Regression (LDSC)
• Version 1.0.1
• (C) 2014-2019 Brendan Bulik-Sullivan and Hilary Finucane
• Broad Institute of MIT and Harvard / MIT Department of Mathematics
• GNU General Public License v3

Call:
./ldsc.py
--h2 BMI.sumstats.gz
--ref-ld-chr 1000G_Phase3_baselineLD_ldscores/baselineLD.
--out BMI.baselineLD
--overlap-annot
--frqfile-chr 1000G_Phase3_frq/1000G.EUR.QC.
--w-ld-chr 1000G_Phase3_weights_hm3_no_MHC/weights.hm3_noMHC.
--print-coefficients
--print-delete-vals

Beginning analysis at Tue Jun 2 11:41:24 2020
Reading summary statistics from BMI.sumstats.gz ...
Read summary statistics for 1040803 SNPs.
Reading reference panel LD Score from 1000G_Phase3_baselineLD_ldscores/baselineLD.[1-22] ...
Error parsing reference panel LD Score.
Traceback (most recent call last):
File "/LDSC/ldsc/ldsc.py", line 644, in
sumstats.estimate_h2(args, log)
File "/LDSC/ldsc/ldscore/sumstats.py", line 329, in estimate_h2
args, log, args.h2)
File "/LDSC/ldsc/ldscore/sumstats.py", line 246, in _read_ld_sumstats
ref_ld = _read_ref_ld(args, log)
File "/LDSC/ldsc/ldscore/sumstats.py", line 85, in _read_ref_ld
'reference panel LD Score', ps.ldscore_fromlist)
File "/LDSC/ldsc/ldscore/sumstats.py", line 158, in _read_chr_split_files
raise e
ValueError: No objects to concatenate