pandas.errors.EmptyDataError: No columns to parse from file

Hi,

When I run vcontact2 on the test-dataset, I got this error.

Command line used: vcontact2 --raw-proteins VIRSorter_genome.faa --rel-mode 'Diamond' -p VIRSorter_genome_g2g.csv --db 'ProkaryoticViralRefSeq94-Merged' --output-dir test_vcontact_out --c1-bin /home/nico/miniconda3/envs/vContact2/bin/

When I test the path of cluster_one: java -jar /home/nico/miniconda3/envs/vContact2/bin/cluster_one-1.0.jar -v ClusterONE 1.0

Error I got: INFO:vcontact2.contig_clusters: Exporting for ClusterONE INFO:vcontact2.contig_clusters: Clustering the PC Similarity-Network using ClusterONE ERROR:vcontact2: Error in contig clustering ERROR:vcontact2: No columns to parse from file Traceback (most recent call last): File "/home/nico/miniconda3/envs/vContact2/bin/vcontact2", line 615, in main gc = vcontact2.contig_clusters.ContigCluster(pcp, output_dir, cluster_one_fp, cluster_one_args, File "/home/nico/miniconda3/envs/vContact2/lib/python3.8/site-packages/vcontact2/contig_clusters.py", line 91, in init self.clusters, self.cluster_results = self.one_cluster(os.path.join(self.folder, self.name), File "/home/nico/miniconda3/envs/vContact2/lib/python3.8/site-packages/vcontact2/contig_clusters.py", line 227, in one_cluster return self.load_one_clusters(fi_clusters) File "/home/nico/miniconda3/envs/vContact2/lib/python3.8/site-packages/vcontact2/contig_clusters.py", line 318, in load_one_clusters clusters_df = pd.read_csv(one_fn, header=0) File "/home/nico/.local/lib/python3.8/site-packages/pandas/io/parsers.py", line 605, in read_csv return _read(filepath_or_buffer, kwds) File "/home/nico/.local/lib/python3.8/site-packages/pandas/io/parsers.py", line 457, in _read parser = TextFileReader(filepath_or_buffer, kwds) File "/home/nico/.local/lib/python3.8/site-packages/pandas/io/parsers.py", line 814, in init self._engine = self._make_engine(self.engine) File "/home/nico/.local/lib/python3.8/site-packages/pandas/io/parsers.py", line 1045, in _make_engine return mappingengine # type: ignore[call-arg] File "/home/nico/.local/lib/python3.8/site-packages/pandas/io/parsers.py", line 1893, in init self._reader = parsers.TextReader(self.handles.handle, kwds) File "pandas/_libs/parsers.pyx", line 521, in pandas._libs.parsers.TextReader.cinit pandas.errors.EmptyDataError: No columns to parse from file

If I run without indicating the path (using all defaults param): vcontact2 --raw-proteins VIRSorter_genome.faa --rel-mode 'Diamond' -p VIRSorter_genome_g2g.csv --db 'ProkaryoticViralRefSeq94-Merged' --output-dir test_vcontact_out

============================This is vConTACT2 0.9.19============================

----------------------------------Pre-Analysis---------------------------------- ERROR:vcontact2: Could not find ClusterONE java file. INFO:vcontact2: Found Diamond: /home/nico/miniconda3/envs/vContact2/bin/diamond INFO:vcontact2: Found MCL: /home/nico/miniconda3/envs/vContact2/bin/mcxload INFO:vcontact2: Identified 14 CPUs INFO:vcontact2: Using reference database: ProkaryoticViralRefSeq94-Merged INFO:vcontact2: Using existing directory test_vcontact_out.

Any idea of what I am doing wrong? Even when I added the file in my $PATH, the file is not found...

Thanks for your help,

Nico

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