map file for BEAGLE imputation

Question

[rachael.kane]

Hello Community,

I am having an issue with BEAGLE V5.2 throwing an error stating all my loci have the same genetic position when they most certainly do not. I have posted the error and a sample of the top of the map file I am using for clarity. I work with non-model organisms without a high quality reference genome so I found a way to list these data in the map file so all loci are in ascending order and used different contigs as different chromosomes instead since BEAGLE needs the map file in ascending order which it is not when the actual chromosome names are used. Let me know if there's something I am missing here but I thought I checked all the boxes as to what BEAGLE requires and I am a bit lost. Any insight is appreciated thank you!

1   834412208350    0   208350  
1   834412239581    0   239581  
1   834412239674    0   239674  
1   834412756751    0   756751  
1   834412756759    0   756759  
1   834412879296    0   879296  
1   8344121188640   0   1188640 
2   834416207087    0   207087  
3   834417968430    0   968430  
3   8344172538197   0   2538197 
3   8344173631447   0   3631447 
3   8344173631533   0   3631533 
4   834418641842    0   641842  
5   834420406910    0   406910  
6   834422242188    0   242188  
7   834423945581    0   945581  
7   8344232263110   0   2263110 
8   8344241023742   0   1023742 
9   834426612563    0   612563  
10  834427966769    0   966769  
10  8344271499303   0   1499303 
11  834428276419    0   276419  
11  834428359973    0   359973  
11  834428783512    0   783512  
12  834430206556    0   206556

Exception in thread "main" java.lang.IllegalArgumentException: All loci in genetic map have the same genetic position [0.0]: 1                           834412208350     0       208350

[rachael.kane]

FYI: super weird formatting issue with the post all chromosomes (#'s 1 -12) are on new lines.

[Duy]

I don't know whether you have already figured this out yet but the third column should be the genetic position of your marker (in cM unit). That's why BEAGLE identified all your loci were in the same genetic position (0).