Index error: list index out of range

[ariannafontanesi]

I am trying to calculate the heritability using the Baseline GRCh38 v1.2 and some ldscores files that I computed on a new personal annotation. I am running this command:

python ldsc.py --h2 sumstats_dir/ --ref-ld-chr baseline_dir/baseline.,baseline_dir/personal_baseline. --w-ld-chr weigths_dir --frqfile-chr plink_dir --overlap-annot --print-coefficients --out outdir

and I get an index error "IndexError: list index out of range" at line 162 of parse.py in ldscore " first_fh = sub_chr(fh, chrs[0]) + suffix". The baseline_dir folder contains .l2.ldscores.gz, .M, .M_5_50 and .annot.gz for both the GRCh38 baseline and my personal annotation. Do you know how I can solve this? Thanks.

[megatron-uk]

@ariannafontanesi - I've just had the same issue trying to follow the example after building a container runtime for ldsc for use by some of the researchers I support.

I believe the issue is a lack of trailing '/' on the --ref-ld-chr and --w-ld-chr arguments.

Without a trailing slash:

Call: 
./ldsc.py \
--h2 /opt/data/BBJ_HDLC22.sumstats.gz \
--ref-ld-chr /opt/data/eas_ldscores \
--w-ld-chr /opt/data/eas_ldscores 

Beginning analysis at Tue Mar 24 21:53:05 2026
Reading summary statistics from /opt/data/BBJ_HDLC22.sumstats.gz ...
RuntimeWarning: compression has no effect when passing a non-binary object as input for file /opt/data/BBJ_HDLC22.sumstats.gz
Read summary statistics for 61663 SNPs.
Reading reference panel LD Score from /opt/data/eas_ldscores[1-22] ... (ldscore_fromlist)
############ list index out of range
Traceback (most recent call last):
  File "/opt/ldsc/ldsc.py", line 640, in <module>
    sumstats.estimate_h2(args, log)
  File "/opt/ldsc/ldscore/sumstats.py", line 320, in estimate_h2
    M_annot, w_ld_cname, ref_ld_cnames, sumstats, novar_cols = _read_ld_sumstats(
  File "/opt/ldsc/ldscore/sumstats.py", line 238, in _read_ld_sumstats
    ref_ld = _read_ref_ld(args, log)
  File "/opt/ldsc/ldscore/sumstats.py", line 74, in _read_ref_ld
    ref_ld = _read_chr_split_files(args.ref_ld_chr, args.ref_ld, log,
  File "/opt/ldsc/ldscore/sumstats.py", line 146, in _read_chr_split_files
    out = parsefunc(_splitp(chr_arg), _N_CHR, **kwargs)
  File "/opt/ldsc/ldscore/parse.py", line 121, in ldscore_fromlist
    y = ldscore(fh, num)
  File "/opt/ldsc/ldscore/parse.py", line 162, in ldscore
    first_fh = sub_chr(fh, chrs[0]) + suffix
IndexError: list index out of range

With the trailing slash:

Call: 
./ldsc.py \
--h2 /opt/data/BBJ_HDLC22.sumstats.gz \
--ref-ld-chr /opt/data/eas_ldscores/ \
--w-ld-chr /opt/data/eas_ldscores/ 

Beginning analysis at Tue Mar 24 21:55:04 2026
Reading summary statistics from /opt/data/BBJ_HDLC22.sumstats.gz ...
RuntimeWarning: compression has no effect when passing a non-binary object as input for file /opt/data/BBJ_HDLC22.sumstats.gz
Read summary statistics for 61663 SNPs.
Reading reference panel LD Score from /opt/data/eas_ldscores/[1-22] ... (ldscore_fromlist)
Read reference panel LD Scores for 1208050 SNPs.
Removing partitioned LD Scores with zero variance.
Reading regression weight LD Score from /opt/data/eas_ldscores/[1-22] ... (ldscore_fromlist)
Read regression weight LD Scores for 1208050 SNPs.
After merging with reference panel LD, 14193 SNPs remain.
After merging with regression SNP LD, 14193 SNPs remain.
WARNING: number of SNPs less than 200k; this is almost always bad.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.2747 (0.1014)
Lambda GC: 1.2103
Mean Chi^2: 1.2826
Intercept: 0.9211 (0.051)
Ratio < 0 (usually indicates GC correction).
Analysis finished at Tue Mar 24 21:55:06 2026
Total time elapsed: 2.18s

I haven't dug through the code yet, but I am going to guess that its where those directories are being parsed for the files within, and the code is likely assuming that the trailing slash will always be there; it's not, and then causes the file finding code to return an empty list (hence the list index out of range error - the list of files is empty).