Bacsort
Bacsort copied to clipboard
cluster_genera.py fails for one genus
Dear Ryan, thanks for developing Bacsort. I'm trying to run it on a bunch of genomes from isolates and cluster_genera.py fails every time, but I can't interpret the error. Do you have any ideas or did anyone ran into that issue before? Thanks in advance!
`Clustering Streptococcus
Loading distances... found 6275 assemblies
Traceback (most recent call last):
File "/home/xyz/Bacsort/scripts/cluster_genera.py", line 221, in
Same kind of error with Enteroroccus clade
command
singularity exec -B /media/:/media/ ~/Bureau/Tools/Bacsort/Bacsort.simg combine_distance_matrices.py tree/fastani.phylip tree/mash.phylip > tree/distances.phylip && singularity exec -B /media/:/media/ ~/Bureau/Tools/Bacsort/Bacsort.simg bionj_tree.R tree/distances.phylip tree/tree.newick
log
This script will create a distance matrix using a combination of distances from
tree/fastani.phylip and tree/mash.phylip. Short distances will come from
tree/fastani.phylip and longer distances from tree/mash.phylip, with
intermediate distances a blend between the two. To ensure a smooth transition
between them, a linear regression will be used to adjust tree/mash.phylip
distances to match those from tree/fastani.phylip.
Loading tree/fastani.phylip (790 assemblies)....... done
Loading tree/mash.phylip (790 assemblies)....... done
Traceback (most recent call last):
File "/usr/local/Bacsort/scripts/combine_distance_matrices.py", line 189, in <module>
main()
File "/usr/local/Bacsort/scripts/combine_distance_matrices.py", line 37, in main
assert matrix_1_assemblies == matrix_2_assemblies
AssertionError