"NaN beta value seen",the pvalues and/or SNP ids are not in order in the output file"

[yeswzc]

my phenotype data is numeric,like
FID IID T7
BT07 BT07 2.866666667
BT09 BT09 4.566666667
BT24 BT24 4.266666667
BT32 BT32 6.8
BT87 BT87 3.033333333
BT88 BT88 8.133333333
BT97 BT97 5.1
B106 B106 7.9
B127 B127 4.733333333
B152 B152 5.6
B203 B203 4.966666667
B214 B214 5.066666667
B221 B221 8.933333333
B233 B233 8.7
B259 B259 7.933333333
B261 B261 8.666666667
CX255 CX255 4.166666667

==the STDOUT/STDERR is:

WARNING:root:NaN beta value seen, may be due to an SNC (a constant SNP)
WARNING:root:NaN beta value seen, may be due to an SNC (a constant SNP)
WARNING:root:NaN beta value seen, may be due to an SNC (a constant SNP)
WARNING:root:NaN beta value seen, may be due to an SNC (a constant SNP)
WARNING:root:NaN beta value seen, may be due to an SNC (a constant SNP)
WARNING:root:NaN beta value seen, may be due to an SNC (a constant SNP)
WARNING:root:NaN beta value seen, may be due to an SNC (a constant SNP)
WARNING:root:NaN beta value seen, may be due to an SNC (a constant SNP)
WARNING:root:NaN beta value seen, may be due to an SNC (a constant SNP)
WARNING:root:NaN beta value seen, may be due to an SNC (a constant SNP)
WARNING:root:NaN beta value seen, may be due to an SNC (a constant SNP)
WARNING:root:NaN beta value seen, may be due to an SNC (a constant SNP)
Optimization restart 1/3, f: nan
Optimization restart 2/3, f: nan
Optimization restart 3/3, f: nan
Iteration: 1, significant SNPs: 0, included SNPs: 0, heritability: 0.0000, f: nan
Optimization restart 1/3, f: nan
Optimization restart 2/3, f: nan
Optimization restart 3/3, f: nan
Iteration: 2, significant SNPs: 0, included SNPs: 1, heritability: 0.0000, f: nan
Optimization restart 1/3, f: nan
Optimization restart 2/3, f: nan
Optimization restart 3/3, f: nan
Iteration: 3, significant SNPs: 0, included SNPs: 2, heritability: 0.0000, f: nan
Optimization restart 1/3, f: nan
Optimization restart 2/3, f: nan
Optimization restart 3/3, f: nan
Iteration: 4, significant SNPs: 0, included SNPs: 3, heritability: 0.0000, f: nan
Optimization restart 1/3, f: nan
Optimization restart 2/3, f: nan
Optimization restart 3/3, f: nan
Iteration: 5, significant SNPs: 0, included SNPs: 4, heritability: 0.0000, f: nan
Optimization restart 1/3, f: nan
Optimization restart 2/3, f: nan
Optimization restart 3/3, f: nan
Iteration: 6, significant SNPs: 0, included SNPs: 5, heritability: 0.0000, f: nan
Optimization restart 1/3, f: nan
Optimization restart 2/3, f: nan
Optimization restart 3/3, f: nan
Iteration: 7, significant SNPs: 0, included SNPs: 6, heritability: 0.0000, f: nan
Optimization restart 1/3, f: nan
Optimization restart 2/3, f: nan
Optimization restart 3/3, f: nan
Iteration: 8, significant SNPs: 0, included SNPs: 7, heritability: 0.0000, f: nan
Optimization restart 1/3, f: nan
Optimization restart 2/3, f: nan
Optimization restart 3/3, f: nan
Iteration: 9, significant SNPs: 0, included SNPs: 8, heritability: 0.0000, f: nan
Optimization restart 1/3, f: nan
Optimization restart 2/3, f: nan
Optimization restart 3/3, f: nan
Iteration: 10, significant SNPs: 0, included SNPs: 9, heritability: 0.0000, f: nan
Optimization restart 1/3, f: nan
Optimization restart 2/3, f: nan
Optimization restart 3/3, f: nan
Iteration: 11, significant SNPs: 0, included SNPs: 10, heritability: 0.0000, f: nan
Traceback (most recent call last):
File "/mnt/215G/software/anaconda2/lib/python2.7/runpy.py", line 162, in _run_module_as_main
"main", fname, loader, pkg_name)
File "/mnt/215G/software/anaconda2/lib/python2.7/runpy.py", line 72, in _run_code
exec code in run_globals
File "/mnt/215G/software/anaconda2/lib/python2.7/site-packages/WarpedLMM-0.21-py2.7.egg/warpedlmm/main.py", line 64, in
util.write_results_to_file(snp_data, pv, results_file_name)
File "/mnt/215G/software/anaconda2/lib/python2.7/site-packages/WarpedLMM-0.21-py2.7.egg/warpedlmm/util/util.py", line 43, in write_results_to_file
assert np.all(results.index == snp_data.sid) and np.all(results['p-value'] == pv), "the pvalues and/or SNP ids are not in order in the output file"
AssertionError: the pvalues and/or SNP ids are not in order in the output file