error: unexpected end-of-file.

[zhujack8]

I ran vcf2phylip to generate the phylip file and got an error:

error: unexpected end-of-file.

After checking the .phy file and found the length of name + padding is not equal 9, which is not 10 that is required by dnapars. After I manually padded the name to 10, the problem is gone.

[edgardomortiz]

Sorry, I don't understand the issue, dnapars gave the error? I have never used that program, could you share a sample of your vcf to see if I can do something?

Edgardo

[zhujack8]

Sorry for the confusing. I meant I used the .phy file from vcf2phylip as input to run PHYLIP dnapars. I got the error. Then I found the problem was that the length of sample name + padding was not equal 10 in the .phy file from vcf2phylip. After I manually padded the name to 10, the problem was gone.