ComplexWarning and RuntimeWarning

[phycochow]

Hello, we have a working version of the tool. As we scale it up, we wanted to report two bugs we encountered, hoping to understand what they mean.

Bug 1 that crashes the program:
INFO:root:log_message(AnnotUnivariateParams(_pi: 1.0, _sig2_beta: 0.05088680883609533, _s: -0.25, _l: -0.274693537774505, _sig2_zeroA: 0.9257157885851576, _sig2_zeroL: 0.0, _p_annot: 1, _p_gene: 1, _n_annot: 76, _n_genes: 144650))
INFO:root:log_message(Computing hessian for 13043 genes on chr 1)
/tools/mixer/precimed/mixer/cli.py:1647: ComplexWarning: Casting complex values to real discards the imaginary part
neg_hess_chr[nonSPD_index, nonSPD_index] = eig_value_min
Traceback (most recent call last):
File "/tools/mixer/precimed/mixer.py", line 16, in
args.func(args)
File "/tools/mixer/precimed/mixer/cli.py", line 1649, in execute_plsa_parser
neg_hess_chr_inv = np.linalg.inv(neg_hess_chr)
File "<array_function internals>", line 180, in inv
File "/usr/local/lib/python3.10/site-packages/numpy/linalg/linalg.py", line 552, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
File "/usr/local/lib/python3.10/site-packages/numpy/linalg/linalg.py", line 89, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix

Bug 2 that is in the log file but doesn't cause observable issues:
INFO:root:log_message(Loading /scratch/project/palpant_scratch/CSYChow/Shim_EpiCop_24/1_Mixer_Annots/1_GenesWithRoI__H3K9ac_Feature_23.tsv with --go-extend-bp=0...)
INFO:root:log_message(Annotating SNPs to GO gene-sets...)
INFO:root:log_message(Done, annotation matrix has 262679 non-zero entries across 141123 SNP and 144650 GO terms)
/tools/mixer/precimed/mixer/cli.py:1436: RuntimeWarning: invalid value encountered in divide
gene_enrich = np.divide(np.divide(gene_h2[0, :], total_h2), np.divide(gene_h2_base, total_h2_base))
/usr/local/lib/python3.10/site-packages/numpy/core/_methods.py:265: RuntimeWarning: Degrees of freedom <= 0 for slice
ret = _var(a, axis=axis, dtype=dtype, out=out, ddof=ddof,
/usr/local/lib/python3.10/site-packages/numpy/core/_methods.py:223: RuntimeWarning: invalid value encountered in divide
arrmean = um.true_divide(arrmean, div, out=arrmean, casting='unsafe',
/usr/local/lib/python3.10/site-packages/numpy/core/_methods.py:254: RuntimeWarning: invalid value encountered in divide
ret = um.true_divide(
INFO:root:log_message(Enrichment results for /scratch/project/palpant_scratch/CSYChow/Shim_EpiCop_24/1_Mixer_Annots/1_GenesWithRoI_Annot__H3K9ac_Feature_23.tsv are saved to /scratch/project/palpant_scratch/CSYChow/Shim_EpiCop_24/4_Mixer_results/F23/formatted_GCST90278514_imp.sumstat_full.go_test_enrich.csv)