0 % of model's snps used

[kys21207]

I am not sure why I keep getting '0 % of model's snps used' even though I used a different model_db.
please the below.

GWAS data: /opt/notebooks/data/ms_all_comers_age_onset.input1.txt.gz
rsid CHROM ALT REF Z P
chr1_791100_G_GGGA_b38 1 GGGA G 0.845756 0.397689
chr1_791101_T_G_b38 1 G T -0.849942 0.395356
...

(imlabtools) root@c7333c32b925:/opt/notebooks# /opt/notebooks/MetaXcan/software/SPrediXcan.py \

--model_db_path /mnt/project/publically_available_supporting_files/scPrediXcan/immune_model/CD4-positive_alpha-beta_cytotoxic_T_cell.db
--covariance /mnt/project/publically_available_supporting_files/scPrediXcan/immune_model/CD4-positive_alpha-beta_cytotoxic_T_cell_covariances.txt.gz
--gwas_folder /opt/notebooks/data/
--gwas_file_pattern ".*gz"
--snp_column rsid
--effect_allele_column ALLELE0
--non_effect_allele_column ALLELE1
--zscore_column Z
--pvalue_column P
--gwas_N 26111
--output_file /opt/notebooks/results/test1.csv
WARNING - Missing --gwas_h2 and --gwas_N are required to calibrate the pvalue and zscore.
INFO - Processing GWAS command line parameters
INFO - Building beta for ms_all_comers_age_onset.input1.txt.gz and /mnt/project/publically_available_supporting_files/scPrediXcan/immune_model/CD4-positive_alpha-beta_cytotoxic_T_cell.db
INFO - Reading input gwas with special handling: /opt/notebooks/data/ms_all_comers_age_onset.input1.txt.gz
INFO - Processing input gwas
INFO - Aligning GWAS to models
INFO - Trimming output
INFO - Successfully parsed input gwas in 16.92726573500113 seconds
INFO - Started metaxcan process
INFO - Loading model from: /mnt/project/publically_available_supporting_files/scPrediXcan/immune_model/CD4-positive_alpha-beta_cytotoxic_T_cell.db
INFO - Loading covariance data from: /mnt/project/publically_available_supporting_files/scPrediXcan/immune_model/CD4-positive_alpha-beta_cytotoxic_T_cell_covariances.txt.gz
INFO - Processing loaded gwas
INFO - Started metaxcan association
INFO - 0 % of model's snps used
WARNING - IMPORTANT: The pvalue and zscore are uncalibrated for inflation
INFO - Sucessfully processed metaxcan association in 860.1160493219995 seconds

[kys21207]

Should I need --gwas_h2 and gwas_N? Without them, SPrediXcan.py gave Warning message.

[Fnyasimi]

Add the flag --keep_non_rsid because in your summary stats you are not using rsid. The two flags above are used to correct for inflation with the newer models as described here