after gwas_parsing.py(liftover), only 10% snp

[Davidseye]

when use code to liftover to hg38,
here is my code:
python /public/home/qihangm/sp.twas/summary-gwas-imputation-master/src/gwas_parsing.py \

-gwas_file /public/home/qihangm/sp.twas/gwas/cp/finngen_R10_K11_CHRONPANC.all
-liftover /public/home/qihangm/sp.twas/liftover/hg19ToHg38.over.chain.gz
-output_column_map rsids variant_id
-output_column_map ref non_effect_allele
-output_column_map alt effect_allele
-output_column_map beta effect_size
-output_column_map pval pvalue
-output_column_map sebeta standard_error
-output_column_map pos position
-output_column_map chrom chromosome
--chromosome_format
-output_column_map af_alt frequence
--insert_value sample_size 196881
-snp_reference_metadata /public/home/qihangm/sp.twas/variant_metadata.txt.gz METADATA
-output_order variant_id panel_variant_id chromosome position effect_allele non_effect_allele frequency pvalue zscore effect_size standard_error sample_size
-output_column_map af_alt frequence
-output /public/home/qihangm/sp.twas/gwas/cp/cp.txt

I only get :

only 10% snp left .
interestingly, when i use the same code to another gwas file (from UKB) ,it works well
is the problem about my data' source? it's from finngen R10 gwas.