Question: MACH Fatal Error Conflict with Previous Genotype
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gravatar for mcburch
6 months ago by
mcburch0
mcburch0 wrote:

I am getting the following error when trying to run MACH on a ped and data file:

WARNING: no reference haplotypes provided. Count number of markers in the sample marker information file ... Read 2697948 markers from sample marker information file WARNING -- Trailing columns in pedigree file will be ignored Expecting 5395896 data columns (2697948 markers [x2 cols]) However line 1, for example, has 5395899 data columns

FATAL ERROR - Conflict with previous genotype - Col 56359, Marker rs140441755 Family: NA18525 Individual: NA18525 Old: 2/2 New: 2/1

The command I am running is "./mach1 -p file.ped -d file.dat --prefix round1. I am not sure what is particularly happening since this same file works fine with other imputation software so maybe the format I have is just not conformant to MACH but I am not sure. Any help is appreciated!

snp software error • 247 views
ADD COMMENTlink modified 6 months ago • written 6 months ago by mcburch0
0
gravatar for mcburch
6 months ago by
mcburch0
mcburch0 wrote:

I found it was an issue with repeated markers.

ADD COMMENTlink written 6 months ago by mcburch0
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