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Description
I ran LogDate using dates.txt and tree.txt and got the following:
Launching LogDate version 1.3.1
LogDate was called as follow
/home/niema/.local/bin/LogDate.py -i tree.txt -t dates.txt -o dated.txt
Finished initialization with random seed 634
Initial state:
mu = 3.249965465691546e-06
fx = 118.93459514305636
Traceback (most recent call last):
File "/home/niema/.local/bin/LogDate.py", line 109, in <module>
mu,f,x,s_tree,t_tree = logDate_with_random_init(tree,f_obj,sampling_time=sampling_time,root_age=rootAge,leaf_age=leafAge,nrep=nrep,min_nleaf=10,maxIter=maxIter,seed=randseed,pseudo=pseudo,seqLen=seqLen,verbose=verbose)
File "/home/niema/.local/bin/LogDate/logdate/logD_lib.py", line 338, in logDate_with_random_init
_,f,x = logIt(tree,smpl_times,f_obj,root_age=root_age,x0=x0,maxIter=maxIter,scale=scale,pseudo=pseudo,seqLen=seqLen,verbose=verbose)
File "/home/niema/.local/bin/LogDate/logdate/logD_lib.py", line 228, in logIt
print("Maximum constraint violation: " + str(np.max(csr_matrix(cons_eq).dot(x_init))))
File "/usr/local/lib/python3.6/dist-packages/scipy/sparse/base.py", line 363, in dot
return self * other
File "/usr/local/lib/python3.6/dist-packages/scipy/sparse/base.py", line 499, in __mul__
raise ValueError('dimension mismatch')
ValueError: dimension mismatch
My sample dates are in unit of days since 0001-01-01. Thoughts?
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