ERROR:vcontact2: No columns to parse from file

[Former user]

ERROR:vcontact2: Error in contig clustering ERROR:vcontact2: No columns to parse from file Traceback (most recent call last): File "/mnt/data/home/lyj/miniconda2/envs/vContac2/bin/vcontact2", line 607, in main gc = vcontact2.contig_clusters.ContigCluster(pcp, output_dir, cluster_one_fp, cluster_one_args, File "/mnt/data/home/lyj/miniconda2/envs/vContac2/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 "/mnt/data/home/lyj/miniconda2/envs/vContac2/lib/python3.8/site-packages/vcontact2/contig_clusters.py", line 227, in one_cluster return self.load_one_clusters(fi_clusters) File "/mnt/data/home/lyj/miniconda2/envs/vContac2/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 "/mnt/data/home/lyj/miniconda2/envs/vContac2/lib/python3.8/site-packages/pandas/io/parsers.py", line 685, in parser_f return _read(filepath_or_buffer, kwds) File "/mnt/data/home/lyj/miniconda2/envs/vContac2/lib/python3.8/site-packages/pandas/io/parsers.py", line 457, in _read parser = TextFileReader(fp_or_buf, kwds) File "/mnt/data/home/lyj/miniconda2/envs/vContac2/lib/python3.8/site-packages/pandas/io/parsers.py", line 895, in init self._make_engine(self.engine) File "/mnt/data/home/lyj/miniconda2/envs/vContac2/lib/python3.8/site-packages/pandas/io/parsers.py", line 1135, in _make_engine self._engine = CParserWrapper(self.f, self.options) File "/mnt/data/home/lyj/miniconda2/envs/vContac2/lib/python3.8/site-packages/pandas/io/parsers.py", line 1917, in init self._reader = parsers.TextReader(src, **kwds) File "pandas/_libs/parsers.pyx", line 545, in pandas._libs.parsers.TextReader.cinit

[Ben Bolduc]

This is likely due to an error related to ClusterONE. Either the ClusterOne java file was not found or there was a problem during its handling of the input data. Ensure that the full path to the c1-bin is specified, or it’s placed in your $PATH.

[Ben Bolduc]

Issue likely stemming from ClusterONE (not installed, or error running). Please re-open if the problem persists.

[fadwa mehdaoui]

Hello, i have the same problem but none of the proposed solutions worked. I do give the full path to c1-bin.

ERROR:vcontact2: Error in contig clustering

ERROR:vcontact2: No columns to parse from file

Traceback (most recent call last):

File "/project/6007483/software/env_vcontact/bin/vcontact2", line 615, in main

gc = vcontact2.contig_clusters.ContigCluster(pcp, output_dir, cluster_one_fp, cluster_one_args,

File "/project/6007483/software/env_vcontact/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 "/project/6007483/software/env_vcontact/lib/python3.8/site-packages/vcontact2/contig_clusters.py", line 227, in one_cluster

return self.load_one_clusters(fi_clusters)

File "/project/6007483/software/env_vcontact/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 "/project/6007483/software/env_vcontact/lib/python3.8/site-packages/pandas/io/parsers.py", line 685, in parser_f

return _read(filepath_or_buffer, kwds)

File "/project/6007483/software/env_vcontact/lib/python3.8/site-packages/pandas/io/parsers.py", line 457, in _read

parser = TextFileReader(fp_or_buf, **kwds)

File "/project/6007483/software/env_vcontact/lib/python3.8/site-packages/pandas/io/parsers.py", line 895, in __init__

self._make_engine(self.engine)

File "/project/6007483/software/env_vcontact/lib/python3.8/site-packages/pandas/io/parsers.py", line 1135, in _make_engine

self._engine = CParserWrapper(self.f, **self.options)

File "/project/6007483/software/env_vcontact/lib/python3.8/site-packages/pandas/io/parsers.py", line 1917, in __init__

self._reader = parsers.TextReader(src, **kwds)

File "pandas/_libs/parsers.pyx", line 545, in pandas._libs.parsers.TextReader.__cinit__

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

[智睿 曹]

Hi, I have the same problem too, and I have written the full path to my $PATH. But it doesn't work. If you have solved this problem, can you give me some advice? Thank you !