Error: No entries in demo_shared.txt correspond to loaded sample IDs.

[jjan...@gmail.com]

The error info showed up when trying gwas for chr 22 using below command:

  plink2 \
    --vcf chr21_shared.vcf.gz dosage=DS \
    --pheno demo_shared.tsv \
    --pheno-name CC \
    --covar demo_shared.tsv \
    --covar-name AGE sex PC1 PC2 PC3 PC4 PC5 \
    --maf 0.001 \
    --glm hide-covar cols=chrom,pos,ref,alt,alt1,a1freq,beta,se,p,nobs,a1freqcc,a1freqcc,machr2 \
    --freq cols=chrom,pos,ref,alt,alt1,alt1freq,machr2,nobs \
    --out chr21_gwas
   

Part of the error info includes:

--vcf: 493472 variants scanned.
--vcf: chr21_gwas-temporary.pgen + chr21_gwas-temporary.pvar.zst +
chr21_gwas-temporary.psam written.
11538 samples (0 females, 0 males, 11538 ambiguous; 11538 founders) loaded from
chr21_gwas-temporary.psam.
493472 variants loaded from chr21_gwas-temporary.pvar.zst.
Error: No entries in demo_shared.txt correspond to loaded sample IDs.

This happened with columns of the demo_shared.txt separated either with tabs or spaces. Same IIDs like R200000348_R200000348 and R200032613_R200032613 exist in the VCF and demographic files.

Can anyone help me out?

Thanks,

[Chris Chang]

- In general, you should always post the FULL .log file when asking for troubleshooting help.  By definition, there's something important you don't know, and in particular you don't know what parts of the .log that you've excluded might help someone else figure out the problem.

- In this case, read the Sample ID conversion section of the PLINK 2.0 documentation.

--
You received this message because you are subscribed to the Google Groups "plink2-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to plink2-users...@googlegroups.com.
To view this discussion visit https://groups.google.com/d/msgid/plink2-users/976c2c9e-65f2-4086-a58c-b022c0b0540en%40googlegroups.com.