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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.
The text was updated successfully, but these errors were encountered:
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
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
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:
The text was updated successfully, but these errors were encountered: