hess.py \
--bfile ./1kg_eur_1pct/1kg_eur_1pct_chr1 \
--partition ./ldetect-data/EUR/fourier_ls-chr1.bed \
--out ./data/step1_pcoschr1 \
--chrom 1 \
--local-hsqg ./data/pcos.txt
/home/limanchao/hess/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 133 partitions on chromosome 1
[INFO] Average window size is 1873901
/home/limanchao/hess/src/refpanel.py:61: FutureWarning: read_table is deprecated, use read_csv instead, passing sep='\t'.
names=['SNP', 'BP', 'A0', 'A1'])
[INFO] 670954 SNPs read from reference panel
[ERROR] Missing column SNP
Thank you
/home/limanchao/hess/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 133 partitions on chromosome 1
[INFO] Average window size is 1873901
/home/limanchao/hess/src/refpanel.py:61: FutureWarning: read_table is deprecated, use read_csv instead, passing sep='\t'.
names=['SNP', 'BP', 'A0', 'A1'])
[INFO] 670954 SNPs read from reference panel
[ERROR] Missing column SNP
Thank you