0 SNPs left after filtering

[lijunpeng-albert]

I am using standard format data for step1 analysis, but all the SNPs are filtered out. I have run many batches of data and this is the only one that has this problem, can you help me? Below is my data and the reported error:

head(bip)
SNP A1 A2 freq b se P N Z BP CHR
1 rs11009607 A G 0.79515 0.009395722 0.0119 0.42780 413466 0.7895564 34258488 10
2 rs12217716 A G 0.59820 0.005703703 0.0096 0.55680 413466 0.5941357 34144725 10
3 rs9417264 A G 0.85320 0.013202463 0.0134 0.32690 413466 0.9852584 38117570 10
4 rs2008617 A T 0.96910 0.015400797 0.0283 0.58530 413466 0.5441978 34459338 10
5 rs2799453 G A 0.38655 -0.007800344 0.0097 0.42130 413466 -0.8041591 34437906 10
6 rs12762493 G A 0.65900 -0.017899240 0.0098 0.06622 413466 -1.8264530 35471873 10

[INFO] @----------------------------------------------------------@
| HESS | v0.5 | 9/October/2017 |
|----------------------------------------------------------|
| (C) 2017 Huwenbo Shi, GNU General Public License, v3 |
|----------------------------------------------------------|
| For documentation, citation & bug-report instructions: |
| http://bogdan.bioinformatics.ucla.edu/software/hess/ |
@----------------------------------------------------------@
[INFO] Command started at: Tue, 25 Jun 2024 17:23:52
[INFO] Command issued:
/public/home/lijunpeng/HESS/hess-0.5.3-beta/hess.py
--bfile /public/home/lijunpeng/HESS/1kg_eur_1pct/1kg_eur_1pct_chr17
--local-rhog /public/home/lijunpeng/HESS/pgc-bip2021-all-new.HESS.txt /public/home/lijunpeng/HESS/DivD_EUR_HESS.txt
--partition /public/home/lijunpeng/HESS/ldetect-data/EUR/fourier_ls-all.bed
--out /public/home/lijunpeng/HESS/Cleandata/BIP/covariance_correlation/step1/BIP_DivD_step1
--chrom 17
/public/home/lijunpeng/HESS/hess-0.5.3-beta/src/refpanel.py:13: FutureWarning: read_table is deprecated, use read_csv instead, passing sep='\t'.
partition = pd.read_table(filename, delim_whitespace=True)
[INFO] Loaded 47 partitions on chromosome 17
[INFO] Average window size is 1727550
/public/home/lijunpeng/HESS/hess-0.5.3-beta/src/refpanel.py:61: FutureWarning: read_table is deprecated, use read_csv instead, passing sep='\t'.
names=['SNP', 'BP', 'A0', 'A1'])
[INFO] 232368 SNPs read from reference panel
[INFO] Loaded 443549 SNPs with rs IDs and single-letter alleles on chromosome 17 from the GWAS summary data file
[INFO] 0 SNPs left after filtering
[INFO] Loaded 175967 SNPs with rs IDs and single-letter alleles on chromosome 17 from the GWAS summary data file
[INFO] 149422 SNPs left after filtering
[INFO] Loading fam file /public/home/lijunpeng/HESS/1kg_eur_1pct/1kg_eur_1pct_chr17.fam
[INFO] Loading bim file /public/home/lijunpeng/HESS/1kg_eur_1pct/1kg_eur_1pct_chr17.bim
/public/home/lijunpeng/miniforge3/envs/HESS/lib/python2.7/site-packages/pysnptools/snpreader/snpreader.py:676: FutureWarning: Method .as_matrix will be removed in a future version. Use .values instead.
pos = fields.as_matrix([0,2,3])
/public/home/lijunpeng/miniforge3/envs/HESS/lib/python2.7/site-packages/pysnptools/snpreader/snpreader.py:625: FutureWarning: Conversion of the second argument of issubdtype from str to str is deprecated. In future, it will be treated as np.string_ == np.dtype(str).type.
assert np.issubdtype(self._row.dtype, str) and len(self._row.shape)==2 and self._row.shape[1]==2, "iid should be dtype str, have two dimensions, and the second dimension should be size 2"
/public/home/lijunpeng/miniforge3/envs/HESS/lib/python2.7/site-packages/pysnptools/snpreader/snpreader.py:626: FutureWarning: Conversion of the second argument of issubdtype from str to str is deprecated. In future, it will be treated as np.string_ == np.dtype(str).type.
assert np.issubdtype(self._col.dtype, str) and len(self._col.shape)==1, "sid should be of dtype of str and one dimensional"
[INFO] bed file is open /public/home/lijunpeng/HESS/1kg_eur_1pct/1kg_eur_1pct_chr17.bed
[INFO] 0 SNPs in locus chr17:56-1172399
[INFO] 0 SNPs in locus chr17:1172399-1928731
[INFO] 0 SNPs in locus chr17:1928731-3702312
[INFO] 0 SNPs in locus chr17:3702312-4696261
[INFO] 0 SNPs in locus chr17:4696261-5741334
[INFO] 0 SNPs in locus chr17:5741334-7317398
[INFO] 0 SNPs in locus chr17:7317398-8306425
[INFO] 0 SNPs in locus chr17:8306425-9965921
[INFO] 0 SNPs in locus chr17:9965921-11102815
[INFO] 0 SNPs in locus chr17:11102815-12534769
[INFO] 0 SNPs in locus chr17:12534769-13180372
[INFO] 0 SNPs in locus chr17:13180372-13894637
[INFO] 0 SNPs in locus chr17:13894637-15019097
[INFO] 0 SNPs in locus chr17:15019097-16412342
[INFO] 0 SNPs in locus chr17:16412342-18856320
[INFO] 0 SNPs in locus chr17:18856320-21290357
[INFO] 0 SNPs in locus chr17:21290357-27334244
[INFO] 0 SNPs in locus chr17:27334244-29786491
[INFO] 0 SNPs in locus chr17:29786491-31538425
[INFO] 0 SNPs in locus chr17:31538425-32912798
[INFO] 0 SNPs in locus chr17:32912798-34469036
[INFO] 0 SNPs in locus chr17:34469036-36809344
[INFO] 0 SNPs in locus chr17:36809344-38877404
[INFO] 0 SNPs in locus chr17:38877404-39899810
[INFO] 0 SNPs in locus chr17:39899810-41772087
[INFO] 0 SNPs in locus chr17:41772087-43056905
[INFO] 0 SNPs in locus chr17:43056905-45876022
[INFO] 0 SNPs in locus chr17:45876022-47517400
[INFO] 0 SNPs in locus chr17:47517400-49898957
[INFO] 0 SNPs in locus chr17:49898957-50719055
[INFO] 0 SNPs in locus chr17:50719055-51826118
[INFO] 0 SNPs in locus chr17:51826118-53599432
[INFO] 0 SNPs in locus chr17:53599432-55357541
[INFO] 0 SNPs in locus chr17:55357541-57487512
[INFO] 0 SNPs in locus chr17:57487512-59312755
[INFO] 0 SNPs in locus chr17:59312755-61545589
[INFO] 0 SNPs in locus chr17:61545589-63148128
[INFO] 0 SNPs in locus chr17:63148128-64800430
[INFO] 0 SNPs in locus chr17:64800430-67858770
[INFO] 0 SNPs in locus chr17:67858770-69387817
[INFO] 0 SNPs in locus chr17:69387817-72672203
[INFO] 0 SNPs in locus chr17:72672203-74375560
[INFO] 0 SNPs in locus chr17:74375560-76263413
[INFO] 0 SNPs in locus chr17:76263413-77298636
[INFO] 0 SNPs in locus chr17:77298636-78837588
[INFO] 0 SNPs in locus chr17:78837588-80034408
[INFO] 0 SNPs in locus chr17:80034408-81194908
[INFO] Command finished at: Tue, 25 Jun 2024 17:25:28