ERROR:vcontact2: Error in contig clustering

[Former user]

While running found the error during clustering. The same error was found when using the test_data

------------------------Contig Clustering & Affiliation------------------------- Loaded graph with 11960 nodes and 252898 edges [====================] 100% Growing clusters from seeds... [====================] 100% Finding highly overlapping clusters... [====================] 100% Merging highly overlapping clusters... Detected 2719 complexes ERROR:vcontact2: Error in contig clustering ERROR:vcontact2: 'DataFrame' object has no attribute 'ix' Traceback (most recent call last): File "/home/gabrielfernandes/miniconda2/envs/vContact2/bin/vcontact", line 607, in main gc = vcontact.contig_clusters.ContigCluster(pcp, output_dir, cluster_one_fp, cluster_one_args, File "/home/gabrielfernandes/miniconda2/envs/vContact2/lib/python3.8/site-packages/vcontact/contig_clusters.py", line 102, in init self.matrix["B"] = matrices.bool_membership(self.contigs) File "/home/gabrielfernandes/miniconda2/envs/vContact2/lib/python3.8/site-packages/vcontact/matrices.py", line 70, in bool_membership xy = contigs.reset_index().ix[:, ["pos", "pos_cluster"]].dropna(subset=["pos_cluster"]).values # pos?, # membership File "/home/gabrielfernandes/miniconda2/envs/vContact2/lib/python3.8/site-packages/pandas/core/generic.py", line 5274, in getattr return object.getattribute(self, name) AttributeError: 'DataFrame' object has no attribute 'ix'

[Gabriel Fernandes]

Install a version of pandas < 1.0

conda install -y -c conda-forge pandas=0.25.3

[Ben Bolduc]

Thanks for responding!

[Ben Bolduc]

Duplicate issue. Resolved by downgrading pandas <1.0. Installation from source code reflects this change, as does the latest package from the Anaconda Bioconda repository.