lcrawlab / i-LDSC

Code and simulations using interaction-LD score regression
https://dataverse.harvard.edu/dataset.xhtml?persistentId=doi:10.7910/DVN/W6MA8J
GNU General Public License v3.0
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Index out of range #1

Open msarguru opened 3 months ago

msarguru commented 3 months ago

Hi, thank you for the iLDSC. Trying it on a sumstat.gz that works for LDSC, returns the index out of range error. and I am using the following syntax. Any suggestions, would be greatly appreciated. ./ldsc.py \ --h2 ../sumstats/PSS.EUR.pdt10.nomerge.sumstats.gz \ --ref-ld-chr ./EUR_1000G/Full_cisLD/ \ --out WMH_EUR_ildsc \ --w-ld-chr ../ldsc/eur_w_ld_chr/ \ --print-coefficients

Beginning analysis at Wed Aug 14 20:19:44 2024 Reading summary statistics from ../sumstats/PSS.EUR.pdt10.nomerge.sumstats.gz ... Read summary statistics for 5355832 SNPs. Reading reference panel LD Score from ./EUR_1000G/Full_cisLD/[1-22] ... (ldscore_fromlist) Traceback (most recent call last): File "ildsc.py", line 651, in sumstats.estimate_h2(args, log) File "/annotation/ldsc-F/ildsc/ldscore/sumstats.py", line 329, in estimate_h2 args, log, args.h2) File "/annotation/ldsc-F/ildsc/ldscore/sumstats.py", line 245, in _read_ld_sumstats ref_ld = _read_ref_ld(args, log) File "/annotation/ldsc-F/ildsc/ldscore/sumstats.py", line 82, in _read_ref_ld 'reference panel LD Score', ps.ldscore_fromlist) File "/annotation/ldsc-F/ildsc/ldscore/sumstats.py", line 154, in _read_chr_split_files out = parsefunc(_splitp(chr_arg), _N_CHR, **kwargs) File "/annotation/ldsc-F/ildsc/ldscore/parse.py", line 103, in ldscore_fromlist y = ldscore(fh, num) File "/annotation/ldsc-F/ildsc/ldscore/parse.py", line 147, in ldscore first_fh = sub_chr(fh, chrs[0]) + suffix IndexError: list index out of range

Analysis finished at Wed Aug 14 20:19:53 2024 Total time elapsed: 9.15s Traceback (most recent call last): File "ildsc.py", line 651, in sumstats.estimate_h2(args, log) File "/annotation/ldsc-F/ildsc/ldscore/sumstats.py", line 329, in estimate_h2 args, log, args.h2) File "/annotation/ldsc-F/ildsc/ldscore/sumstats.py", line 245, in _read_ld_sumstats ref_ld = _read_ref_ld(args, log) File "/annotation/ldsc-F/ildsc/ldscore/sumstats.py", line 82, in _read_ref_ld 'reference panel LD Score', ps.ldscore_fromlist) File "/annotation/ldsc-F/ildsc/ldscore/sumstats.py", line 154, in _read_chr_split_files out = parsefunc(_splitp(chr_arg), _N_CHR, **kwargs) File "/annotation/ldsc-F/ildsc/ldscore/parse.py", line 103, in ldscore_fromlist y = ldscore(fh, num) File "/annotation/ldsc-F/ildsc/ldscore/parse.py", line 147, in ldscore first_fh = sub_chr(fh, chrs[0]) + suffix IndexError: list index out of range

msarguru commented 3 months ago

Update. Got this sorted, turned out issue with the filenaming.. also few suggestions on the readme for git.. one has to use git sparse-checkout set --no-cone * to get all the required ldscore files.

Would love an addition on the interpretation of the output.. what each column refers to, etc. Thanks again