Help with value error

[boxiangliu]

Hello Anil,

I am using qtlBHM to finemap eQTLs and get enrichment scores for annotations. I am getting a strange value error (see below). It seems to be something related to the CVXOPT package. Do you have any idea what would lead to this?

2017-11-12 15:39:44 loaded test statistics from ../processed_data/sqtl/fastQTL/enrichment/chr10.statistics.txt.gz
2017-11-12 15:40:18 loaded genomic annotations from ../processed_data/sqtl/fastQTL/snpEff//all.2.bed.gz
2017-11-12 15:44:52 preprocessed data.
2017-11-12 15:45:10 4007 genes; 323656 variants; 3 annotations
2017-11-12 15:45:10 Initial likelihood = nan
Traceback (most recent call last):
File "/srv/persistent/bliu2/tools/qtlBHM/infer_causal_variants.py", line 103, in
data, posteriors, annotation = bhmodel.learn_and_infer(test_statistics, variant_annotations, options.prior_var, options.mintol)
File "bhmodel.pyx", line 345, in bhmodel.learn_and_infer (bhmodel.c:12816)
annotation.update(data, posteriors)
File "bhmodel.pyx", line 130, in bhmodel.Annotation.update (bhmodel.c:5844)
self.weights = optimize_annotation_weights(x_init, data, self.annotvalues, posteriors)
File "bhmodel.pyx", line 160, in bhmodel.optimize_annotation_weights (bhmodel.c:7722)
solution = solvers.cp(F)
File "/srv/persistent/bliu2/tools/anaconda/lib/python2.7/site-packages/cvxopt/cvxprog.py", line 1966, in cp
xdot_e, xaxpy_e, xscal_e, options = options)
File "/srv/persistent/bliu2/tools/anaconda/lib/python2.7/site-packages/cvxopt/cvxprog.py", line 1333, in cpl
misc.update_scaling(W, lmbda, ds, dz)
File "/srv/persistent/bliu2/tools/anaconda/lib/python2.7/site-packages/cvxopt/misc.py", line 450, in update_scaling
s[:m] = base.sqrt( s[:m] )
ValueError: domain error