paturley
commented
4 years ago It looks to me like the software is not able to parse the column names in your summary statistic files. Sometimes it helps to remove any columns from your sum stats files other than those that are required by the MTAG and LDSC software. Does that seem to help?
On Fri, Feb 14, 2020 at 11:19 AM wsproviero notifications@github.com wrote:
Hi, I have git cloned the MTAG directory and created the conda environment. mtag.py works just fine but both ldsc.py and munge_sumstats.py do not work at all. python ldsc.py -h throughs at me this error: Traceback (most recent call last): File "ldsc.py", line 14, in import ldscore.sumstats as sumstats File "/Users/[username]/bin/GWAS_META_LD/try/mtag/ldsc_mod/ldscore/sumstats.py", line 15, in from ldsc_mod.ldscore import parse as ps ImportError: No module named ldsc_mod.ldscore
So I have downloaded ldsc separately and substituted the ldsc existing package with the one downloaded from the github official page.
I run the commands with no problem until mtag throughs at me the following error: [.......] Conversion finished at Fri Feb 14 16:04:16 2020 Total time elapsed: 59.44s
<><><<>><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><> Munging of Trait 2 complete. SNPs remaining: 7800735
<><><<>><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>
1202640 strand ambiguous SNPs in Trait 1 are included. 1200758 strand ambiguous SNPs in Trait 2 are included. ... Merge of GWAS summary statistics complete. Number of SNPs: 7788953 Using 6588195 SNPs to estimate Omega (1200758 SNPs excluded due to strand ambiguity) Estimating sigma.. Improperly formatted sumstats file: ('Usecols do not match names.',) Traceback (most recent call last): File "/Users/[username]/bin/GWAS_META_LD/mtag/mtag.py", line 1567, in mtag(args) File "/Users/[username]/bin/GWAS_META_LD/mtag/mtag.py", line 1351, in mtag args.sigma_hat = estimate_sigma(DATA[not_SA], args) File "/Users/[username]/bin/GWAS_META_LD/mtag/mtag.py", line 465, in estimate_sigma rg_results_t = sumstats_sig.estimate_rg(args_ldsc_rg, Logger_to_Logging()) File "/Users/[username]/bin/GWAS_META_LD/mtag/ldsc_mod/ldscore/sumstats.py", line 397, in estimate_rg alleles=True, dropna=True) File "/Users/[username]/bin/GWAS_META_LD/mtag/ldsc_mod/ldscore/sumstats.py", line 242, in _read_ld_sumstats sumstats = _read_sumstats(args, log, fh, alleles=alleles, dropna=dropna) File "/Users/[username]/bin/GWAS_META_LD/mtag/ldsc_mod/ldscore/sumstats.py", line 163, in _read_sumstats sumstats = ps.sumstats(fh, alleles=alleles, dropna=dropna) File "/Users/[username]/bin/GWAS_META_LD/mtag/ldsc_mod/ldscore/parse.py", line 81, in sumstats raise ValueError('Improperly formatted sumstats file: ' + str(e.args)) ValueError: Improperly formatted sumstats file: ('Usecols do not match names.',) Analysis terminated from error at Fri Feb 14 16:08:15 2020 Total time elapsed: 7.0m:0.93s
I have tried to tweak my files several times but the error persists.
Can you help me please? Thank you. William
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wsproviero
Hi, I have git cloned the MTAG directory and created the conda environment. mtag.py works just fine but both ldsc.py and munge_sumstats.py do not work at all. python ldsc.py -h throughs at me this error: Traceback (most recent call last): File "ldsc.py", line 14, in
import ldscore.sumstats as sumstats
File "/Users/[username]/bin/GWAS_META_LD/try/mtag/ldsc_mod/ldscore/sumstats.py", line 15, in
from ldsc_mod.ldscore import parse as ps
ImportError: No module named ldsc_mod.ldscore
So I have downloaded ldsc separately and substituted the ldsc existing package with the one downloaded from the github official page.
I run the commands with no problem until mtag throughs at me the following error: [.......] Conversion finished at Fri Feb 14 16:04:16 2020 Total time elapsed: 59.44s <><><<>><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><> Munging of Trait 2 complete. SNPs remaining: 7800735 <><><<>><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>
1202640 strand ambiguous SNPs in Trait 1 are included. 1200758 strand ambiguous SNPs in Trait 2 are included. ... Merge of GWAS summary statistics complete. Number of SNPs: 7788953 Using 6588195 SNPs to estimate Omega (1200758 SNPs excluded due to strand ambiguity) Estimating sigma.. Improperly formatted sumstats file: ('Usecols do not match names.',) Traceback (most recent call last): File "/Users/[username]/bin/GWAS_META_LD/mtag/mtag.py", line 1567, in
mtag(args)
File "/Users/[username]/bin/GWAS_META_LD/mtag/mtag.py", line 1351, in mtag
args.sigma_hat = estimate_sigma(DATA[not_SA], args)
File "/Users/[username]/bin/GWAS_META_LD/mtag/mtag.py", line 465, in estimate_sigma
rg_results_t = sumstats_sig.estimate_rg(args_ldsc_rg, Logger_to_Logging())
File "/Users/[username]/bin/GWAS_META_LD/mtag/ldsc_mod/ldscore/sumstats.py", line 397, in estimate_rg
alleles=True, dropna=True)
File "/Users/[username]/bin/GWAS_META_LD/mtag/ldsc_mod/ldscore/sumstats.py", line 242, in _read_ld_sumstats
sumstats = _read_sumstats(args, log, fh, alleles=alleles, dropna=dropna)
File "/Users/[username]/bin/GWAS_META_LD/mtag/ldsc_mod/ldscore/sumstats.py", line 163, in _read_sumstats
sumstats = ps.sumstats(fh, alleles=alleles, dropna=dropna)
File "/Users/[username]/bin/GWAS_META_LD/mtag/ldsc_mod/ldscore/parse.py", line 81, in sumstats
raise ValueError('Improperly formatted sumstats file: ' + str(e.args))
ValueError: Improperly formatted sumstats file: ('Usecols do not match names.',)
Analysis terminated from error at Fri Feb 14 16:08:15 2020
Total time elapsed: 7.0m:0.93s
I have tried to tweak my files several times but the error persists.
Can you help me please? Thank you. William