The input files includes 26 linkage groups but the output files only includes 22 linkage group

[yingxins]

The input file was generated by plink, and I checked there are 26 linkage groups with other unaligned scaffold:

> cat bamlist_halfInd_filter_refilter_pheno.bim | cut -f1 |uniq lg01 lg02 lg03 lg04 lg05 lg06 lg07 lg08 lg09 lg10 lg11 lg12 lg13 lg14 lg15 lg16 lg17 lg18 lg19 lg20 lg21 lg22 lg23 lg24 lg25 lg26 scaffold

However, only 22 linkage groups were found in the output files:
cat DS_gemma_GWAS_wald.assoc.txt | cut -f1 | uniq chr lg01 lg02 lg03 lg04 lg05 lg06 lg07 lg08 lg09 lg10 lg11 lg12 lg13 lg14 lg15 lg16 lg17 lg18 lg19 lg20 lg21 lg22

Here is the command that I run to generate input and output:
plink --file $bfile --pheno $phenotype --make-bed --out ${bfile}_pheno --noweb --allow-no-sex --allow-extra-chr gemma -bfile bamlist_halfInd_filter_refilter_pheno -lm 1 -o DS_gemma_GWAS_wald
Any idea what causes it?