Error in contig clustering

[Former user]

Dear developers:

I am encountering the following issue while trying to run vContact2 and I haven´t been able to figure out where exactly is the problem. I'd be very grateful of any insight you may have about it, and thank you for the effort in developing and maintaining this tool. I'm running the following command:

vcontact -r reference_genomes_ORFs_c95.faa --rel-mode 'Diamond' --proteins-fp gene2genome.csv --db 'ArchaeaViralRefSeq97-Merged' --pcs-mode MCL --vcs-mode ClusterONE --c1-bin /corefac/bio/szq311/softwares/cluster_one-1.0.jar --output-dir vContactOut/

Here is the error message:

------------------------Contig Clustering & Affiliation------------------------- Loaded graph with 108 nodes and 1304 edges [====================] 100% Growing clusters from seeds... [====================] 100% Finding highly overlapping clusters... [====================] 100% Merging highly overlapping clusters... Detected 18 complexes ERROR:vcontact2: Error in contig clustering ERROR:vcontact2: 'DataFrame' object has no attribute 'ix' Traceback (most recent call last): File "/usr/local/home/szq311/miniconda3/bin/vcontact", line 607, in main gc = vcontact.contig_clusters.ContigCluster(pcp, output_dir, cluster_one_fp, cluster_one_args, File "/usr/local/home/szq311/miniconda3/lib/python3.9/site-packages/vcontact/contig_clusters.py", line 102, in init self.matrix["B"] = matrices.bool_membership(self.contigs) File "/usr/local/home/szq311/miniconda3/lib/python3.9/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 "/usr/local/home/szq311/miniconda3/lib/python3.9/site-packages/pandas/core/generic.py", line 5487, in getattr return object.getattribute(self, name) AttributeError: 'DataFrame' object has no attribute 'ix'

And here are the intermediate files in the partial output

c1.clusters merged_df.csv merged.faa merged.self-diamond.tab.abc merged.self-diamond.tab_mcl20.clusters vConTACT_contigs.csv vConTACT_profiles.csv c1.ntw
merged.dmnd
merged.self-diamond.tab
merged.self-diamond.tab.mci
merged.self-diamond.tab_mcxload.tab
vConTACT_pcs.csv
vConTACT_proteins.csv

The intermediate output look as expected and I have also tried running vcontact using the contigs, profiles and pcs files and ended up having the same result.

Best, Laura