[3:apply]:
---------------------------------------------------------------------------ValueError Traceback (most recent call last)<string> in <module>()
/home/deren/Documents/ipyrad/ipyrad/assemble/jointestimate.pyc in optim(args)
255 (bfreqs, ustacks, counts),
256 disp=False,
--> 257 full_output=False)
258 return [sample.name, hetero, errors]
259
/home/deren/anaconda/lib/python2.7/site-packages/scipy/optimize/optimize.pyc in fmin(func, x0, args, xtol, ftol, maxiter, maxfun, full_output, disp, retall, callback)
375 'return_all': retall}
376
--> 377 res = _minimize_neldermead(func, x0, args, callback=callback, **opts)
378 if full_output:
379 retlist = res['x'], res['fun'], res['nit'], res['nfev'], res['status']
/home/deren/anaconda/lib/python2.7/site-packages/scipy/optimize/optimize.pyc in _minimize_neldermead(func, x0, args, callback, xtol, ftol, maxiter, maxfev, disp, return_all, **unknown_options)
433 if retall:
434 allvecs = [sim[0]]
--> 435 fsim[0] = func(x0)
436 nonzdelt = 0.05
437 zdelt = 0.00025
/home/deren/anaconda/lib/python2.7/site-packages/scipy/optimize/optimize.pyc in function_wrapper(*wrapper_args)
283 def function_wrapper(*wrapper_args):
284 ncalls[0] += 1
--> 285 return function(*(wrapper_args + args))
286
287 return ncalls, function_wrapper
/home/deren/Documents/ipyrad/ipyrad/assemble/jointestimate.pyc in get_diploid_lik(pstart, bfreqs, ustacks, counts)
94 else:
95 ## get likelihood for all sites
---> 96 lik1 = (1.-hetero)*likelihood1(errors, bfreqs, ustacks)
97 lik2 = (hetero)*likelihood2(errors, bfreqs, ustacks)
98 liks = lik1+lik2
/home/deren/Documents/ipyrad/ipyrad/assemble/jointestimate.pyc in likelihood1(errors, bfreqs, ustacks)
46 ## make sure base_frequencies are in the right order
47 #print uniqstackl.sum()-uniqstack, uniqstackl.sum(), 0.001
---> 48 totals = np.array([ustacks.sum(axis=1)]*4).T
49 prob = scipy.stats.binom.pmf(totals-ustacks, totals, errors)
50 return np.sum(bfreqs*prob, axis=1)
/home/deren/anaconda/lib/python2.7/site-packages/numpy/core/_methods.pyc in _sum(a, axis, dtype, out, keepdims)
30
31 def _sum(a, axis=None, dtype=None, out=None, keepdims=False):
---> 32 return umr_sum(a, axis, dtype, out, keepdims)
33
34 def _prod(a, axis=None, dtype=None, out=None, keepdims=False):
ValueError: 'axis' entry is out of bounds
[0:apply]:
---------------------------------------------------------------------------ValueError Traceback (most recent call last)<string> in <module>()
/home/deren/Documents/ipyrad/ipyrad/assemble/jointestimate.pyc in optim(args)
255 (bfreqs, ustacks, counts),
256 disp=False,
--> 257 full_output=False)
258 return [sample.name, hetero, errors]
259
/home/deren/anaconda/lib/python2.7/site-packages/scipy/optimize/optimize.pyc in fmin(func, x0, args, xtol, ftol, maxiter, maxfun, full_output, disp, retall, callback)
375 'return_all': retall}
376
--> 377 res = _minimize_neldermead(func, x0, args, callback=callback, **opts)
378 if full_output:
379 retlist = res['x'], res['fun'], res['nit'], res['nfev'], res['status']
/home/deren/anaconda/lib/python2.7/site-packages/scipy/optimize/optimize.pyc in _minimize_neldermead(func, x0, args, callback, xtol, ftol, maxiter, maxfev, disp, return_all, **unknown_options)
433 if retall:
434 allvecs = [sim[0]]
--> 435 fsim[0] = func(x0)
436 nonzdelt = 0.05
437 zdelt = 0.00025
/home/deren/anaconda/lib/python2.7/site-packages/scipy/optimize/optimize.pyc in function_wrapper(*wrapper_args)
283 def function_wrapper(*wrapper_args):
284 ncalls[0] += 1
--> 285 return function(*(wrapper_args + args))
286
287 return ncalls, function_wrapper
/home/deren/Documents/ipyrad/ipyrad/assemble/jointestimate.pyc in get_diploid_lik(pstart, bfreqs, ustacks, counts)
94 else:
95 ## get likelihood for all sites
---> 96 lik1 = (1.-hetero)*likelihood1(errors, bfreqs, ustacks)
97 lik2 = (hetero)*likelihood2(errors, bfreqs, ustacks)
98 liks = lik1+lik2
/home/deren/Documents/ipyrad/ipyrad/assemble/jointestimate.pyc in likelihood1(errors, bfreqs, ustacks)
46 ## make sure base_frequencies are in the right order
47 #print uniqstackl.sum()-uniqstack, uniqstackl.sum(), 0.001
---> 48 totals = np.array([ustacks.sum(axis=1)]*4).T
49 prob = scipy.stats.binom.pmf(totals-ustacks, totals, errors)
50 return np.sum(bfreqs*prob, axis=1)
/home/deren/anaconda/lib/python2.7/site-packages/numpy/core/_methods.pyc in _sum(a, axis, dtype, out, keepdims)
30
31 def _sum(a, axis=None, dtype=None, out=None, keepdims=False):
---> 32 return umr_sum(a, axis, dtype, out, keepdims)
33
34 def _prod(a, axis=None, dtype=None, out=None, keepdims=False):
ValueError: 'axis' entry is out of bounds
[1:apply]:
---------------------------------------------------------------------------ValueError Traceback (most recent call last)<string> in <module>()
/home/deren/Documents/ipyrad/ipyrad/assemble/jointestimate.pyc in optim(args)
255 (bfreqs, ustacks, counts),
256 disp=False,
--> 257 full_output=False)
258 return [sample.name, hetero, errors]
259
/home/deren/anaconda/lib/python2.7/site-packages/scipy/optimize/optimize.pyc in fmin(func, x0, args, xtol, ftol, maxiter, maxfun, full_output, disp, retall, callback)
375 'return_all': retall}
376
--> 377 res = _minimize_neldermead(func, x0, args, callback=callback, **opts)
378 if full_output:
379 retlist = res['x'], res['fun'], res['nit'], res['nfev'], res['status']
/home/deren/anaconda/lib/python2.7/site-packages/scipy/optimize/optimize.pyc in _minimize_neldermead(func, x0, args, callback, xtol, ftol, maxiter, maxfev, disp, return_all, **unknown_options)
433 if retall:
434 allvecs = [sim[0]]
--> 435 fsim[0] = func(x0)
436 nonzdelt = 0.05
437 zdelt = 0.00025
/home/deren/anaconda/lib/python2.7/site-packages/scipy/optimize/optimize.pyc in function_wrapper(*wrapper_args)
283 def function_wrapper(*wrapper_args):
284 ncalls[0] += 1
--> 285 return function(*(wrapper_args + args))
286
287 return ncalls, function_wrapper
/home/deren/Documents/ipyrad/ipyrad/assemble/jointestimate.pyc in get_diploid_lik(pstart, bfreqs, ustacks, counts)
94 else:
95 ## get likelihood for all sites
---> 96 lik1 = (1.-hetero)*likelihood1(errors, bfreqs, ustacks)
97 lik2 = (hetero)*likelihood2(errors, bfreqs, ustacks)
98 liks = lik1+lik2
/home/deren/Documents/ipyrad/ipyrad/assemble/jointestimate.pyc in likelihood1(errors, bfreqs, ustacks)
46 ## make sure base_frequencies are in the right order
47 #print uniqstackl.sum()-uniqstack, uniqstackl.sum(), 0.001
---> 48 totals = np.array([ustacks.sum(axis=1)]*4).T
49 prob = scipy.stats.binom.pmf(totals-ustacks, totals, errors)
50 return np.sum(bfreqs*prob, axis=1)
/home/deren/anaconda/lib/python2.7/site-packages/numpy/core/_methods.pyc in _sum(a, axis, dtype, out, keepdims)
30
31 def _sum(a, axis=None, dtype=None, out=None, keepdims=False):
---> 32 return umr_sum(a, axis, dtype, out, keepdims)
33
34 def _prod(a, axis=None, dtype=None, out=None, keepdims=False):
ValueError: 'axis' entry is out of bounds
[2:apply]:
---------------------------------------------------------------------------ValueError Traceback (most recent call last)<string> in <module>()
/home/deren/Documents/ipyrad/ipyrad/assemble/jointestimate.pyc in optim(args)
255 (bfreqs, ustacks, counts),
256 disp=False,
--> 257 full_output=False)
258 return [sample.name, hetero, errors]
259
/home/deren/anaconda/lib/python2.7/site-packages/scipy/optimize/optimize.pyc in fmin(func, x0, args, xtol, ftol, maxiter, maxfun, full_output, disp, retall, callback)
375 'return_all': retall}
376
--> 377 res = _minimize_neldermead(func, x0, args, callback=callback, **opts)
378 if full_output:
379 retlist = res['x'], res['fun'], res['nit'], res['nfev'], res['status']
/home/deren/anaconda/lib/python2.7/site-packages/scipy/optimize/optimize.pyc in _minimize_neldermead(func, x0, args, callback, xtol, ftol, maxiter, maxfev, disp, return_all, **unknown_options)
433 if retall:
434 allvecs = [sim[0]]
--> 435 fsim[0] = func(x0)
436 nonzdelt = 0.05
437 zdelt = 0.00025
/home/deren/anaconda/lib/python2.7/site-packages/scipy/optimize/optimize.pyc in function_wrapper(*wrapper_args)
283 def function_wrapper(*wrapper_args):
284 ncalls[0] += 1
--> 285 return function(*(wrapper_args + args))
286
287 return ncalls, function_wrapper
/home/deren/Documents/ipyrad/ipyrad/assemble/jointestimate.pyc in get_diploid_lik(pstart, bfreqs, ustacks, counts)
94 else:
95 ## get likelihood for all sites
---> 96 lik1 = (1.-hetero)*likelihood1(errors, bfreqs, ustacks)
97 lik2 = (hetero)*likelihood2(errors, bfreqs, ustacks)
98 liks = lik1+lik2
/home/deren/Documents/ipyrad/ipyrad/assemble/jointestimate.pyc in likelihood1(errors, bfreqs, ustacks)
46 ## make sure base_frequencies are in the right order
47 #print uniqstackl.sum()-uniqstack, uniqstackl.sum(), 0.001
---> 48 totals = np.array([ustacks.sum(axis=1)]*4).T
49 prob = scipy.stats.binom.pmf(totals-ustacks, totals, errors)
50 return np.sum(bfreqs*prob, axis=1)
/home/deren/anaconda/lib/python2.7/site-packages/numpy/core/_methods.pyc in _sum(a, axis, dtype, out, keepdims)
30
31 def _sum(a, axis=None, dtype=None, out=None, keepdims=False):
---> 32 return umr_sum(a, axis, dtype, out, keepdims)
33
34 def _prod(a, axis=None, dtype=None, out=None, keepdims=False):
ValueError: 'axis' entry is out of bounds
... 8 more exceptions ...