TypeError: '<' not supported between instances of 'float' and 'str'

[ReneKat]

Hello hclust2 community,
I am running on Windows Subsystem Linux Ubuntu 20. hclust2 was installed using conda
conda install -c bioconda hclust2
conda update hclust2

$ hclust2.py -i abundance_table_species.txt -o abundance_heatmap_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
Traceback (most recent call last):
  File "/home/renekat/anaconda3/envs/phlan/bin/hclust2.py", line 825, in <module>
    hclust2_main()
  File "/home/renekat/anaconda3/envs/phlan/bin/hclust2.py", line 784, in hclust2_main
    dm = DataMatrix( args.inp, args )
  File "/home/renekat/anaconda3/envs/phlan/bin/hclust2.py", line 174, in __init__
    select( self.args.fperc, self.args.ftop )
  File "/home/renekat/anaconda3/envs/phlan/bin/hclust2.py", line 159, in select
    self.table['perc'] = self.table.apply(lambda x: stats.scoreatpercentile(x,perc),axis=1)
  File "/home/renekat/anaconda3/envs/phlan/lib/python3.7/site-packages/pandas/core/frame.py", line 6878, in apply
    return op.get_result()
  File "/home/renekat/anaconda3/envs/phlan/lib/python3.7/site-packages/pandas/core/apply.py", line 186, in get_result
    return self.apply_standard()
  File "/home/renekat/anaconda3/envs/phlan/lib/python3.7/site-packages/pandas/core/apply.py", line 296, in apply_standard
    values, self.f, axis=self.axis, dummy=dummy, labels=labels
  File "pandas/_libs/reduction.pyx", line 620, in pandas._libs.reduction.compute_reduction
  File "pandas/_libs/reduction.pyx", line 128, in pandas._libs.reduction.Reducer.get_result
  File "/home/renekat/anaconda3/envs/phlan/bin/hclust2.py", line 159, in <lambda>
    self.table['perc'] = self.table.apply(lambda x: stats.scoreatpercentile(x,perc),axis=1)
  File "/home/renekat/anaconda3/envs/phlan/lib/python3.7/site-packages/scipy/stats/stats.py", line 1891, in scoreatpercentile
    sorted_ = np.sort(a, axis=axis)
  File "<__array_function__ internals>", line 6, in sort
  File "/home/renekat/anaconda3/envs/phlan/lib/python3.7/site-packages/numpy/core/fromnumeric.py", line 989, in sort
    a.sort(axis=axis, kind=kind, order=order)
TypeError: '<' not supported between instances of 'float' and 'str'

Any help with this error would be appreciated!
Best,
Rene

EDITED:
I am not sure if the two errors are related, but I tried to run on the example data and got this:

$ /mnt/c/Users/Student/github/hclust2/examples/HMP-MetaPhlAn/run.sh
Traceback (most recent call last):
  File "/home/renekat/anaconda3/envs/phlan/bin/hclust2.py", line 825, in <module>
    hclust2_main()
  File "/home/renekat/anaconda3/envs/phlan/bin/hclust2.py", line 803, in hclust2_main
    cl.shcluster()
  File "/home/renekat/anaconda3/envs/phlan/bin/hclust2.py", line 380, in shcluster
    self.shclusters = sph.linkage(self.s_dm, method=self.args.slinkage)
  File "/home/renekat/anaconda3/envs/phlan/lib/python3.7/site-packages/scipy/cluster/hierarchy.py", line 1057, in linkage
    raise ValueError("The condensed distance matrix must contain only "
ValueError: The condensed distance matrix must contain only finite values.

[nousiaso]

Hello ReneKat i experience exactly the same issue. And I did exactly what you did and got the same errors. So either our input table is wrong or we miss something

[ReneKat]

Hi @nousiaso,
Since the last line was an error in python I updated the python in my environment
conda update python -y

I just found this answer: biobakery/MetaPhlAn#87

The code i was running is actually different than my previous post:

hclust2.py -i merged_abundance_table.txt -o FCCHH.sqrt_scale.png --skip_rows 1 \
>   --ftop 50 \
>   --f_dist_f correlation \
>   --s_dist_f braycurtis \
>   --cell_aspect_ratio 9 \
>   -s --fperc 99 \
>   --flabel_size 4 \
>   --metadata_rows 2,3,4 \
>   --legend_file HMP.sqrt_scale.legend.png \
>   --max_flabel_len 100 \
>   --metadata_height 0.075 \
>   --minv 0.01 \
>   --no_slabels \
>   --dpi 300 \
>   --slinkage complete

And so when I removed the --skip_rows 1 the code finally ran.
Hopefully you have some success!

[nousiaso]

thanks a lot rene i will try it