Hi! I am fairly new to Metaphlan, so I could use some guidance – I followed these directions with my outputted .txt file:
grep -E “(s__)|(^ID)” /u/home/c/choi/test_metaphlan.txt | grep -v “t__” | sed ‘s/^.*s__//g’ > /u/home/c/choi/test_metaphlan_species.txt
hclust2.py -i /u/home/c/choi/test_metaphlan_species.txt -o /u/home/c/choi/test_metaphlan_species.png --ftop 25 --f_dist_f braycurtis --s_dist_f braycurtis --cell_aspect_ratio 0.5 -l --flabel_size 6 --slabel_size 6 --max_flabel_len 100 --max_slabel_len 100 --minv 0.1 --dpi 300
And I get the following errors:
Traceback (most recent call last):
File “/u/home/c/choi/.conda/envs/mpa/bin/hclust2.py”, line 825, in
hclust2_main()
File “/u/home/c/choi/.conda/envs/mpa/bin/hclust2.py”, line 784, in hclust2_main
dm = DataMatrix( args.inp, args )
File “/u/home/c/choi/.conda/envs/mpa/bin/hclust2.py”, line 174, in init
select( self.args.fperc, self.args.ftop )
File “/u/home/c/choi/.conda/envs/mpa/bin/hclust2.py”, line 159, in select
self.table[‘perc’] = self.table.apply(lambda x: stats.scoreatpercentile(x,perc),axis=1)
File “/u/local/apps/python/3.9.6/gcc-4.8.5/lib/python3.9/site-packages/pandas/core/frame.py”, line 8736, in apply
return op.apply()
File “/u/local/apps/python/3.9.6/gcc-4.8.5/lib/python3.9/site-packages/pandas/core/apply.py”, line 688, in apply
return self.apply_standard()
File “/u/local/apps/python/3.9.6/gcc-4.8.5/lib/python3.9/site-packages/pandas/core/apply.py”, line 812, in apply_standard
results, res_index = self.apply_series_generator()
File “/u/local/apps/python/3.9.6/gcc-4.8.5/lib/python3.9/site-packages/pandas/core/apply.py”, line 828, in apply_series_generator
results[i] = self.f(v)
File “/u/home/c/choi/.conda/envs/mpa/bin/hclust2.py”, line 159, in
self.table[‘perc’] = self.table.apply(lambda x: stats.scoreatpercentile(x,perc),axis=1)
File “/u/local/apps/python/3.9.6/gcc-4.8.5/lib/python3.9/site-packages/scipy/stats/stats.py”, line 1825, in scoreatpercentile
sorted_ = np.sort(a, axis=axis)
File “<array_function internals>”, line 180, in sort
File “/u/local/apps/python/3.9.6/gcc-4.8.5/lib/python3.9/site-packages/numpy/core/fromnumeric.py”, line 1004, in sort
a.sort(axis=axis, kind=kind, order=order)
TypeError: ‘<’ not supported between instances of ‘float’ and ‘str’