Plink error message: Misaligned SNPs in dosage files

Question

[hessjl]

Hi all,

I'm trying to run a mega-GWAS of multiple studies in Plink and came across the following error message:

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Skipping web check... [ --noweb ]
Writing this text to log file [ GWASoutput.log ]

Options in effect:

    --noweb
    --dosage combineDOS.txt
      list
    --fam combined.fam
    --assoc
    --out GWASoutput

Reading pedigree information from [ combined.fam ] 
3771 individuals read from [ combined.fam ] 
3771 individuals with nonmissing phenotypes
Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
Missing phenotype value is also -9
1058 cases, 2713 controls and 0 missing
2714 males, 1057 females, and 0 of unspecified sex

Reading dosage information from [ combineDOS.txt ]
Format set to two genotype probabilities
Expecting 7 total files, in 0 distinct batches of SNPs
Writing results to [ GWASoutput.assoc.dosage ]
Matched to 3125 of 3771 individuals in 7 files
Removed 646 individuals not in dosage file

**ERROR: Misaligned SNPs in dosage files**

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If this error message is familiar, please provide me with an explanation. I'm stumped!

Sincerest gratitude,

Jon