lsdc :IndexError: list index out of range

[chirrie]

I am try to generate LD scores using below command

./ldsc.py
--ref-ld-chr LDSCORE.1000G_AFR.tab.gz
--out FG_T2D24
--rg FG.sumstats.gz,T2D_EUR.sumstats.gz
--w-ld-chr LDSCORE.1000G_AFR.tab.gz

I get below error
File "/home/chebii/Awi-gen/FG_raw/boltlmm/ldsc/ldscore/sumstats.py", line 397, in estimate_rg
alleles=True, dropna=True)
File "/home/chebii/Awi-gen/FG_raw/boltlmm/ldsc/ldscore/sumstats.py", line 243, in _read_ld_sumstats
ref_ld = _read_ref_ld(args, log)
File "/home/chebii/Awi-gen/FG_raw/boltlmm/ldsc/ldscore/sumstats.py", line 82, in _read_ref_ld
'reference panel LD Score', ps.ldscore_fromlist)
File "/home/chebii/Awi-gen/FG_raw/boltlmm/ldsc/ldscore/sumstats.py", line 152, in _read_chr_split_files
out = parsefunc(_splitp(chr_arg), _N_CHR, **kwargs)
File "/home/chebii/Awi-gen/FG_raw/boltlmm/ldsc/ldscore/parse.py", line 103, in ldscore_fromlist
y = ldscore(fh, num)
File "/home/chebii/Awi-gen/FG_raw/boltlmm/ldsc/ldscore/parse.py", line 147, in ldscore
first_fh = sub_chr(fh, chrs[0]) + suffix
IndexError: list index out of range

[sophk1]

I am getting the same error, using the same flags. Have you been able to find a solution?

[chirrie]

No, not yet. it seems it is a common problem but no solution

…

On Tue, Mar 12, 2024 at 8:57 PM sophk1 ***@***.***> wrote: I am getting the same error, using the same flags. Have you been able to find a solution? — Reply to this email directly, view it on GitHub <#421 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAZTQ2XLARWKKTHYUVKXHC3YX5FYFAVCNFSM6AAAAABEOXKSOGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSOJSGMZTSMBSGI> . You are receiving this because you authored the thread.Message ID: ***@***.***>

-- Vivien Chebii, Ph.D. Post doctoral Scientist (Bioinformatics) Sydney Brenner Institute for Molecular Biosciences, Wits University, South Africa Email: ***@***.*** ***@***.***>*; ***@***.*** Mobile: +254 722 712 248 Linkedin: www.linkedin.com/in/viviennechebii/

[mvab]

most likely you forgot to download the ref files; the provided links in README don't work. Download it from here: https://zenodo.org/records/8182036 and tar -jxvf eur_w_ld_chr.tar.gz

[chirrie]

The reference works for non_European cohort as well. My assumption was that I will.ise the reference from respective ancestry of the study cohort

…

On Fri, 5 Apr 2024, 17:52 Marina Vabistsevits, ***@***.***> wrote: most likely you forgot to download the ref files; the provided links in README don't work. Download it from here: https://zenodo.org/records/8182036 and tar -jxvf eur_w_ld_chr.tar.gz — Reply to this email directly, view it on GitHub <#421 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAZTQ2WS6QOCJ2XNOOYU5UDY323CPAVCNFSM6AAAAABEOXKSOGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANBQGAYDCMBVG4> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[aksarkar]

@chirrie You need to use --ref-ld and --w-ld, not --ref-ld-chr and --w-ld-chr

The flags -chr are for input files that are split by chromosome.

[chirrie]

Thanks , let me try

…

On Sun, 5 May 2024, 23:25 Abhishek Sarkar, ***@***.***> wrote: @chirrie <https://github.com/chirrie> You need to use --ref-ld and --w-ld, not --ref-ld-chr and --w-ld-chr The flags -chr are for input files that are split by chromosome. — Reply to this email directly, view it on GitHub <#421 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAZTQ2QH3KX7WOEH3DPAVMDZA2IURAVCNFSM6AAAAABEOXKSOGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAOJUHEZTONBRHA> . You are receiving this because you were mentioned.Message ID: ***@***.***>