Hi all,

I have used the vcftools to filter my data some weeks ago, and it went smoothly. However, I run the vcftools with the same vcf file again recently, it gets the following warnings:

Using zlib version: 1.2.8
Warning: Expected at least 2 parts in FORMAT entry: ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another">
Warning: Expected at least 2 parts in FORMAT entry: ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group">
Warning: Expected at least 2 parts in FORMAT entry: ID=RGQ,Number=1,Type=Integer,Description="Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)">
Warning: Expected at least 2 parts in INFO entry: ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
Warning: Expected at least 2 parts in INFO entry: ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
Warning: Expected at least 2 parts in INFO entry: ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
Warning: Expected at least 2 parts in INFO entry: ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
Warning: Expected at least 2 parts in INFO entry: ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">
Warning: Expected at least 2 parts in INFO entry: ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">
Warning: Expected at least 2 parts in INFO entry: ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts, for each ALT allele, in the same order as listed">
Warning: Expected at least 2 parts in INFO entry: ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts, for each ALT allele, in the same order as listed">
Warning: Expected at least 2 parts in INFO entry: ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">
Warning: Expected at least 2 parts in INFO entry: ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">
Warning: Expected at least 2 parts in INFO entry: ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency, for each ALT allele, in the same order as listed">
Warning: Expected at least 2 parts in INFO entry: ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency, for each ALT allele, in the same order as listed">
Warning: Expected at least 2 parts in INFO entry: ID=culprit,Number=1,Type=String,Description="The annotation which was the worst performing in the Gaussian mixture model, likely the reason why the variant was filtered out">
After filtering, kept 19 out of 19 Individuals
Outputting VCF file...
After filtering, kept 1539040 out of a possible 1679429 Sites
Run Time = 86.00 seconds

I have no idea about why it shows so many warnings this time, for previously using the same vcf did not get such warnings. Could anyone help me?

Thank you!