Error installing via conda

[Jigyasa3]

Hey @alneberg!

I am following the documentation on CONCOCT installation via conda, and I am running into python error. I have tried removing the environment and reinstalling it, but the error prevails. I have concoct version 1.0 installed after re-installation.

Code- concoct --composition_file ${IN_DIR}/Scaffolds.fasta --coverage_file ${COVERAGE_DIR}/Feature-Matrix-concoct.txt -b ${OUT_DIR}/

Error- Up and running. Check /flash/BourguignonU/Jigs/binning/concoct_272may1_MAL39/log.txt for progress /home/j/jigyasa-arora/miniconda2/envs/concoct_env/lib/python3.6/site-packages/concoct/input.py:90: FutureWarning: .ix is deprecated. Please use .loc for label based indexing or .iloc for positional indexing

See the documentation here: http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated cov.ix[:,cov_range[0]:cov_range[1]] = cov.ix[:,cov_range[0]:cov_range[1]].add( /home/j/jigyasa-arora/miniconda2/envs/concoct_env/lib/python3.6/site-packages/pandas/core/indexing.py:822: FutureWarning: .ix is deprecated. Please use .loc for label based indexing or .iloc for positional indexing

See the documentation here: http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated retval = getattr(retval, self.name)._getitem_axis(key, axis=i) /home/j/jigyasa-arora/miniconda2/envs/concoct_env/lib/python3.6/site-packages/concoct/input.py:92: FutureWarning: .ix is deprecated. Please use .loc for label based indexing or .iloc for positional indexing

See the documentation here: http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated axis='index') /home/j/jigyasa-arora/miniconda2/envs/concoct_env/lib/python3.6/site-packages/concoct/input.py:97: FutureWarning: .ix is deprecated. Please use .loc for label based indexing or .iloc for positional indexing

See the documentation here: http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated _normalize_per_sample(cov.ix[:,cov_range[0]:cov_range[1]]) /home/j/jigyasa-arora/miniconda2/envs/concoct_env/lib/python3.6/site-packages/concoct/input.py:102: FutureWarning: .ix is deprecated. Please use .loc for label based indexing or .iloc for positional indexing

See the documentation here: http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated cov['total_coverage'] = cov.ix[:,cov_range[0]:cov_range[1]].sum(axis=1) /home/j/jigyasa-arora/miniconda2/envs/concoct_env/lib/python3.6/site-packages/concoct/input.py:108: FutureWarning: .ix is deprecated. Please use .loc for label based indexing or .iloc for positional indexing

See the documentation here: http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated _normalize_per_contig(cov.ix[:,cov_range[0]:cov_range[1]]) /home/j/jigyasa-arora/miniconda2/envs/concoct_env/lib/python3.6/site-packages/concoct/input.py:115: FutureWarning: .ix is deprecated. Please use .loc for label based indexing or .iloc for positional indexing

See the documentation here: http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated cov.ix[:,cov_range[0]:cov_range[1]]) /home/j/jigyasa-arora/miniconda2/envs/concoct_env/lib/python3.6/site-packages/concoct/input.py:115: RuntimeWarning: divide by zero encountered in log cov.ix[:,cov_range[0]:cov_range[1]]) /home/j/jigyasa-arora/miniconda2/envs/concoct_env/bin/concoct:28: FutureWarning: .ix is deprecated. Please use .loc for label based indexing or .iloc for positional indexing

See the documentation here: http://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#ix-indexer-is-deprecated joined = composition.join(cov.ix[:,cov_range[0]:cov_range[1]],how="inner") Traceback (most recent call last): File "/home/j/jigyasa-arora/miniconda2/envs/concoct_env/bin/concoct", line 88, in results = main(args) File "/home/j/jigyasa-arora/miniconda2/envs/concoct_env/bin/concoct", line 40, in main args.seed File "/home/j/jigyasa-arora/miniconda2/envs/concoct_env/lib/python3.6/site-packages/concoct/transform.py", line 5, in perform_pca pca_object = PCA(n_components=nc, random_state=seed).fit(d) File "/home/j/jigyasa-arora/miniconda2/envs/concoct_env/lib/python3.6/site-packages/sklearn/decomposition/pca.py", line 329, in fit self._fit(X) File "/home/j/jigyasa-arora/miniconda2/envs/concoct_env/lib/python3.6/site-packages/sklearn/decomposition/pca.py", line 370, in _fit copy=self.copy) File "/home/j/jigyasa-arora/miniconda2/envs/concoct_env/lib/python3.6/site-packages/sklearn/utils/validation.py", line 462, in check_array context)) ValueError: Found array with 0 sample(s) (shape=(0, 138)) while a minimum of 1 is required.