All SNPs excluded as multiallelic

Hi, I meeting some problem that all vriants was excluded as multiallelic. This doesn't seem to make sense: 1) It is impossible for multiallelic genes on a certain chromosome; 2) other chromosomes data can be entered without any problems.

Is there any good solution?

2024-01-25 14:33:18 : INFO : running xpclr v1.1.2
2024-01-25 14:33:18 : INFO : Loading TXT
2024-01-25 14:34:04 : INFO : TXT loading complete
2024-01-25 14:34:13 : INFO : 6,388,458 SNPs in total are in the provided input files
2024-01-25 14:34:14 : INFO : 6,388,458 SNPs excluded as multiallelic
2024-01-25 14:34:14 : INFO : 0 SNPs excluded as missing in all samples in a population
2024-01-25 14:34:15 : INFO : 0 SNPs excluded as invariant or singleton in population 2
2024-01-25 14:34:15 : INFO : 0/6,388,458 SNPs included in the analysis (0.00%)
Traceback (most recent call last):
  File "/home/name/anaconda3/envs/xpclr/bin/xpclr", line 196, in <module>
    main()
  File "/home/name/anaconda3/envs/xpclr/bin/xpclr", line 164, in main
    g1 = g1.compress(include, axis=0)
         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/name/anaconda3/envs/xpclr/lib/python3.11/site-packages/allel/model/chunked.py", line 297, in compress
    return compress_genotypes(self, condition, axis=axis, wrap_axes={0, 1},
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/name/anaconda3/envs/xpclr/lib/python3.11/site-packages/allel/model/generic.py", line 180, in compress_genotypes
    out = cls(out)
          ^^^^^^^^
  File "/home/name/anaconda3/envs/xpclr/lib/python3.11/site-packages/allel/model/chunked.py", line 110, in __init__
    check_ndim(self.values, 3)
  File "/home/name/anaconda3/envs/xpclr/lib/python3.11/site-packages/allel/util.py", line 63, in check_ndim
    raise TypeError('bad number of dimensions: expected %s; found %s' % (ndim, a.ndim))
TypeError: bad number of dimensions: expected 3; found 0

hardingnj / xpclr

All SNPs excluded as multiallelic #105