exPAM issueshttps://gitlab.erc.monash.edu.au/ssol0002/pam/-/issues2020-05-04T13:25:57+10:00https://gitlab.erc.monash.edu.au/ssol0002/pam/-/issues/3distance matrix is the 0 matrix error2020-05-04T13:25:57+10:00Vanessa Marcelinodistance matrix is the 0 matrix errorHi Sean!
New interesting error here:
````
New Parent 4...
Length: 5
@timeit join of pam.phylogeny.Index: 15.274498563725501s
@timeit do_pairwise of pam.phylogeny.Phylogeny: 5.173899203073233s
Traceback (most recent call last):
File “bi...Hi Sean!
New interesting error here:
````
New Parent 4...
Length: 5
@timeit join of pam.phylogeny.Index: 15.274498563725501s
@timeit do_pairwise of pam.phylogeny.Phylogeny: 5.173899203073233s
Traceback (most recent call last):
File “bin/make_db.py”, line 97, in <module>
init_phylogeny(ref_url, k, cutoff)
File “bin/make_db.py”, line 57, in init_phylogeny
phylogeny.apply_neighbour_joining()
File “/mnt/lustre/scratch/vmar0011/ref_databases/Murphy_MSBL/pam/pam/phylogeny/Phylogeny.py”, line 71, in apply_neighbour_joining
i, j = self.find_neighbourhood(s_matrix) # i > j.
File “/mnt/lustre/scratch/vmar0011/ref_databases/Murphy_MSBL/pam/pam/phylogeny/Phylogeny.py”, line 185, in find_neighbourhood
raise ValueError(“Distance matrix is the 0 matrix.“)
ValueError: Distance matrix is the 0 matrix.
````
Any clue of what might be causing this?
I run this with k=14 and c=0.8, and a database of 388 genomes.
Thanks!Sean SolariSean Solari