================================================================================================================================================================================= ./plink2 --vcf /home/peixott/beegfs/TopMed/WithoutHWE/chr21.dose.vcf.gz --max-alleles 2 --rm-dup exclude-all --snps-only --make-pgen --maf 0.005 --out ./PFILES/LARGE_chr21_Try2 PLINK v2.00a3LM AVX2 Intel (11 Oct 2021) www.cog-genomics.org/plink/2.0/ (C) 2005-2021 Shaun Purcell, Christopher Chang GNU General Public License v3 Logging to ./PFILES/LARGE_chr21_Try2.log. Options in effect: --maf 0.005 --make-pgen --max-alleles 2 --out ./PFILES/LARGE_chr21_Try2 --rm-dup exclude-all --snps-only --vcf /home/peixott/beegfs/TopMed/WithoutHWE/chr21.dose.vcf.gz Start time: Wed Jan 12 16:42:34 2022 192026 MiB RAM detected; reserving 96013 MiB for main workspace. Using up to 40 threads (change this with --threads). --vcf: 590411 variants scanned. --vcf: ./PFILES/LARGE_chr21_Try2-temporary.pgen + ./PFILES/LARGE_chr21_Try2-temporary.pvar.zst + ./PFILES/LARGE_chr21_Try2-temporary.psam written. 1498 samples (0 females, 0 males, 1498 ambiguous; 1498 founders) loaded from ./PFILES/LARGE_chr21_Try2-temporary.psam. 544741 out of 590411 variants loaded from ./PFILES/LARGE_chr21_Try2-temporary.pvar.zst. Note: No phenotype data present. Note: Skipping --rm-dup since no duplicate IDs are present. Calculating allele frequencies... done. 401892 variants removed due to allele frequency threshold(s) (--maf/--max-maf/--mac/--max-mac). 142849 variants remaining after main filters. Writing ./PFILES/LARGE_chr21_Try2.psam ... done. Writing ./PFILES/LARGE_chr21_Try2.pvar ... done. Writing ./PFILES/LARGE_chr21_Try2.pgen ... done. End time: Wed Jan 12 16:42:52 2022 ================================================================================================================================================================================= admix assoc --pfile ./PFILES/LARGE_chr21_Biallelic_COVAR --pheno ./PFILES/LARGE_chr22_Biallelic_COVAR_pheno.txt --pheno-col DISEASE --method ATT,TRACTOR,SNP1 --out AssocTest21 --family binary --covar ./PFILES/LARGE_chr21_Biallelic_COVAR_covarNonNA.txt 2022-01-12 16:48.12 [info ] Received parameters: assoc --pfile=./PFILES/LARGE_chr21_Biallelic_COVAR --pheno=./PFILES/LARGE_chr22_Biallelic_COVAR_pheno.txt --pheno_col=DISEASE --out=AssocTest21 --covar=./PFILES/LARGE_chr21_Biallelic_COVAR_covarNonNA.txt --method=('ATT', 'TRACTOR', 'SNP1') --family=binary --fast=True 2022-01-12 16:48.12 [info ] admix.Dataset: read local ancestry from ./PFILES/LARGE_chr21_Biallelic_COVAR.lanc 2022-01-12 16:48.13 [info ] admix.Dataset: `n_anc` is not provided, infered n_anc from the first 1,000 SNPs is 3. If this is not correct, provide `n_anc` when constructing admix.Dataset 2022-01-12 16:48.13 [info ] 142849 SNPs and 1480 individuals are loaded 2022-01-12 16:48.13 [warning ] admix.dataset.append_indiv_info: 1/1481 individuals in the new dataframe not in the dataset; These individuals will be ignored. 2022-01-12 16:48.13 [warning ] admix.dataset.append_indiv_info: 1/1481 individuals in the new dataframe not in the dataset; These individuals will be ignored. 2022-01-12 16:48.13 [info ] 12 covariates are loaded: AGE,SEX,PC1,PC2,PC3,PC4,PC5,PC6,PC7,PC8,PC9,PC10 2022-01-12 16:48.13 [info ] 142849 SNPs and 1480 individuals left after filtering for missing phenotype, or completely missing covariate 2022-01-12 16:48.13 [info ] Detected categorical columns: 2022-01-12 16:48.13 [info ] Added dummy variables: 2022-01-12 16:48.13 [info ] Performing association analysis with method ATT admix.assoc.marginal: 6%|██████████▏ | 8/140 [00:25<07:06, 3.23s/it]Warning: [tinygwas.logistic_reg] A fraction of 31% of the observations can be perfectly predicted (abs(y - g) < 1e-4). This might indicate complete quasi-separation. Exiting iterations early and the corresponding loglik is set to NaN /cm/shared/apps/python/3.8.6/lib/python3.8/site-packages/scipy/stats/_distn_infrastructure.py:903: RuntimeWarning: invalid value encountered in greater return (a < x) & (x < b) /cm/shared/apps/python/3.8.6/lib/python3.8/site-packages/scipy/stats/_distn_infrastructure.py:903: RuntimeWarning: invalid value encountered in less return (a < x) & (x < b) /cm/shared/apps/python/3.8.6/lib/python3.8/site-packages/scipy/stats/_distn_infrastructure.py:1912: RuntimeWarning: invalid value encountered in less_equal cond2 = cond0 & (x <= _a) admix.assoc.marginal: 6%|███████████▍ | 9/140 [00:29<07:01, 3.22s/it]Warning: [tinygwas.logistic_reg] A fraction of 15% of the observations can be perfectly predicted (abs(y - g) < 1e-4). This might indicate complete quasi-separation. Exiting iterations early and the corresponding loglik is set to NaN admix.assoc.marginal: 8%|█████████████▉ | 11/140 [00:35<06:51, 3.19s/it]Warning: [tinygwas.logistic_reg] A fraction of 48% of the observations can be perfectly predicted (abs(y - g) < 1e-4). This might indicate complete quasi-separation. Exiting iterations early and the corresponding loglik is set to NaN Warning: [tinygwas.logistic_reg] A fraction of 42% of the observations can be perfectly predicted (abs(y - g) < 1e-4). This might indicate complete quasi-separation. Exiting iterations early and the corresponding loglik is set to NaN Warning: [tinygwas.logistic_reg] A fraction of 34% of the observations can be perfectly predicted (abs(y - g) < 1e-4). This might indicate complete quasi-separation. Exiting iterations early and the corresponding loglik is set to NaN Warning: [tinygwas.logistic_reg] A fraction of 42% of the observations can be perfectly predicted (abs(y - g) < 1e-4). This might indicate complete quasi-separation. Exiting iterations early and the corresponding loglik is set to NaN admix.assoc.marginal: 12%|█████████████████████▍ | 17/140 [00:54<06:34, 3.21s/it]Warning: [tinygwas.logistic_reg] A fraction of 10% of the observations can be perfectly predicted (abs(y - g) < 1e-4). This might indicate complete quasi-separation. Exiting iterations early and the corresponding loglik is set to NaN Warning: [tinygwas.logistic_reg] A fraction of 10% of the observations can be perfectly predicted (abs(y - g) < 1e-4). This might indicate complete quasi-separation. Exiting iterations early and the corresponding loglik is set to NaN admix.assoc.marginal: 24%|██████████████████████████████████████████▉ | 34/140 [01:49<05:44, 3.25s/it]Warning: [tinygwas.logistic_reg] A fraction of 56% of the observations can be perfectly predicted (abs(y - g) < 1e-4). This might indicate complete quasi-separation. Exiting iterations early and the corresponding loglik is set to NaN Warning: [tinygwas.logistic_reg] A fraction of 57% of the observations can be perfectly predicted (abs(y - g) < 1e-4). This might indicate complete quasi-separation. Exiting iterations early and the corresponding loglik is set to NaN Warning: [tinygwas.logistic_reg] A fraction of 57% of the observations can be perfectly predicted (abs(y - g) < 1e-4). This might indicate complete quasi-separation. Exiting iterations early and the corresponding loglik is set to NaN admix.assoc.marginal: 26%|█████████████████████████████████████████████▌ | 36/140 [01:56<05:40, 3.27s/it]Warning: [tinygwas.logistic_reg] A fraction of 7% of the observations can be perfectly predicted (abs(y - g) < 1e-4). This might indicate complete quasi-separation. Exiting iterations early and the corresponding loglik is set to NaN Warning: [tinygwas.logistic_reg] A fraction of 21% of the observations can be perfectly predicted (abs(y - g) < 1e-4). This might indicate complete quasi-separation. Exiting iterations early and the corresponding loglik is set to NaN Warning: [tinygwas.logistic_reg] A fraction of 25% of the observations can be perfectly predicted (abs(y - g) < 1e-4). This might indicate complete quasi-separation. Exiting iterations early and the corresponding loglik is set to NaN admix.assoc.marginal: 27%|████████████████████████████████████████████████ | 38/140 [02:02<05:29, 3.23s/it]Warning: [tinygwas.logistic_reg] A fraction of 8% of the observations can be perfectly predicted (abs(y - g) < 1e-4). This might indicate complete quasi-separation. Exiting iterations early and the corresponding loglik is set to NaN admix.assoc.marginal: 32%|████████████████████████████████████████████████████████▉ | 45/140 [02:25<05:10, 3.27s/it]Warning: [tinygwas.logistic_reg] A fraction of 49% of the observations can be perfectly predicted (abs(y - g) < 1e-4). This might indicate complete quasi-separation. Exiting iterations early and the corresponding loglik is set to NaN admix.assoc.marginal: 44%|██████████████████████████████████████████████████████████████████████████████▍ | 62/140 [03:21<04:14, 3.27s/it]admix.assoc.marginal: 46%|████████████████████████████████████████████████████████████████████████████████▉ | 64/140 [03:28<04:07, 3.26s/it]Traceback (most recent call last): File "/home/peixott/.local/bin/admix", line 33, in sys.exit(load_entry_point('admix-kit', 'console_scripts', 'admix')()) File "/mnt/beegfs/peixott/admix-kit/admix/cli.py", line 542, in cli fire.Fire() File "/home/peixott/.local/lib/python3.8/site-packages/fire/core.py", line 141, in Fire component_trace = _Fire(component, args, parsed_flag_args, context, name) File "/home/peixott/.local/lib/python3.8/site-packages/fire/core.py", line 466, in _Fire component, remaining_args = _CallAndUpdateTrace( File "/home/peixott/.local/lib/python3.8/site-packages/fire/core.py", line 681, in _CallAndUpdateTrace component = fn(*varargs, **kwargs) File "/mnt/beegfs/peixott/admix-kit/admix/cli.py", line 526, in assoc dict_rls[m] = admix.assoc.marginal( File "/mnt/beegfs/peixott/admix-kit/admix/assoc/__init__.py", line 333, in marginal _block_test( File "/mnt/beegfs/peixott/admix-kit/admix/assoc/__init__.py", line 71, in _block_test var = var.compute() File "/home/peixott/.local/lib/python3.8/site-packages/dask/base.py", line 288, in compute (result,) = compute(self, traverse=False, **kwargs) File "/home/peixott/.local/lib/python3.8/site-packages/dask/base.py", line 571, in compute results = schedule(dsk, keys, **kwargs) File "/home/peixott/.local/lib/python3.8/site-packages/dask/threaded.py", line 79, in get results = get_async( File "/home/peixott/.local/lib/python3.8/site-packages/dask/local.py", line 507, in get_async raise_exception(exc, tb) File "/home/peixott/.local/lib/python3.8/site-packages/dask/local.py", line 315, in reraise raise exc File "/home/peixott/.local/lib/python3.8/site-packages/dask/local.py", line 220, in execute_task result = _execute_task(task, data) File "/home/peixott/.local/lib/python3.8/site-packages/dask/core.py", line 119, in _execute_task return func(*(_execute_task(a, cache) for a in args)) File "/home/peixott/.local/lib/python3.8/site-packages/dask/core.py", line 119, in return func(*(_execute_task(a, cache) for a in args)) File "/home/peixott/.local/lib/python3.8/site-packages/dask/core.py", line 119, in _execute_task return func(*(_execute_task(a, cache) for a in args)) File "/home/peixott/.local/lib/python3.8/site-packages/dask/core.py", line 119, in return func(*(_execute_task(a, cache) for a in args)) File "/home/peixott/.local/lib/python3.8/site-packages/dask/core.py", line 119, in _execute_task return func(*(_execute_task(a, cache) for a in args)) File "/home/peixott/.local/lib/python3.8/site-packages/dask/core.py", line 119, in return func(*(_execute_task(a, cache) for a in args)) File "/home/peixott/.local/lib/python3.8/site-packages/dask/core.py", line 119, in _execute_task return func(*(_execute_task(a, cache) for a in args)) File "/home/peixott/.local/lib/python3.8/site-packages/dask/utils.py", line 37, in apply return func(*args, **kwargs) File "/home/peixott/.local/lib/python3.8/site-packages/dapgen/_read.py", line 350, in _read_pgen_chunk pgen.read_alleles_range(snp_start, snp_stop, geno) File "pgenlib.pyx", line 894, in pgenlib.PgenReader.read_alleles_range File "pgenlib.pyx", line 922, in pgenlib.PgenReader.read_alleles_range RuntimeError: variant_idx 65618 read_alleles_range() error 6 admix.assoc.marginal: 46%|████████████████████████████████████████████████████████████████████████████████▉ | 64/140 [03:28<04:07, 3.25s/it] ================================================================================================================================================================================= PVAR (from 65610 to 65630, the 65618 is chr21:27881249:T:C) 21 27879990 chr21:27879990:T:G T G PASS AF=0.80402;MAF=0.19598;R2=0.88338;IMPUTED 21 27880000 chr21:27880000:A:T A T PASS AF=0.00890;MAF=0.00890;R2=0.71623;IMPUTED 21 27880154 chr21:27880154:T:C T C PASS AF=0.39648;MAF=0.39648;R2=0.95035;IMPUTED 21 27880157 chr21:27880157:T:G T G PASS AF=0.35057;MAF=0.35057;R2=0.95835;IMPUTED 21 27880231 chr21:27880231:G:A G A PASS AF=0.40308;MAF=0.40308;R2=0.94712;IMPUTED 21 27880593 chr21:27880593:G:C G C PASS AF=0.02203;MAF=0.02203;R2=0.87242;IMPUTED 21 27880665 chr21:27880665:C:A C A PASS AF=0.37210;MAF=0.37210;R2=0.94602;IMPUTED 21 27880990 chr21:27880990:C:A C A PASS AF=0.01710;MAF=0.01710;R2=0.67903;IMPUTED 21 27881249 chr21:27881249:T:C T C PASS AF=0.00834;MAF=0.00834;R2=0.89633;IMPUTED 21 27881680 chr21:27881680:T:C T C PASS AF=0.07262;MAF=0.07262;R2=0.74558;IMPUTED 21 27881917 chr21:27881917:C:T C T PASS AF=0.00883;MAF=0.00883;R2=0.68973;IMPUTED 21 27882082 chr21:27882082:T:C T C PASS AF=0.35150;MAF=0.35150;R2=0.96071;IMPUTED 21 27882450 chr21:27882450:C:G C G PASS AF=0.35366;MAF=0.35366;R2=0.95895;IMPUTED 21 27882664 chr21:27882664:A:T A T PASS AF=0.04837;MAF=0.04837;R2=0.91591;IMPUTED 21 27883093 chr21:27883093:G:C G C PASS AF=0.38328;MAF=0.38328;R2=0.96856;IMPUTED 21 27884112 chr21:27884112:C:T C T PASS AF=0.02080;MAF=0.02080;R2=0.87386;IMPUTED 21 27884196 chr21:27884196:C:G C G PASS AF=0.96935;MAF=0.03065;R2=0.39020;IMPUTED 21 27884249 chr21:27884249:C:G C G PASS AF=0.38596;MAF=0.38596;R2=0.94927;IMPUTED 21 27884316 chr21:27884316:A:G A G PASS AF=0.27175;MAF=0.27175;R2=0.90328;IMPUTED 21 27884493 chr21:27884493:T:C T C PASS AF=0.38414;MAF=0.38414;R2=0.94897;IMPUTED 21 27884591 chr21:27884591:C:T C T PASS AF=0.81606;MAF=0.18394;R2=0.89289;IMPUTED