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"NaN beta value seen",the pvalues and/or SNP ids are not in order in the output file" #4

Open yeswzc opened 8 years ago

yeswzc commented 8 years ago

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