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borenstein-lab / fishtaco

FishTaco (Functional Shifts Taxonomic Contributors) is a metagenomic computational framework that aims to identify the driver taxa of microbiome functional shifts
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Test File Errors #13

Open aaadeg opened 2 years ago

aaadeg commented 2 years ago

Hello, I am unable to get the test_fishtaco.py file to work... I installed version 1.1.6 and followed the install instructions at https://borenstein-lab.github.io/fishtaco/installation.html . I get about 10 errors when I run the test file. Is there anybody that would be able to assist me? I am not a computer programmer so it's been a huge learning curve trying to learn to code and run this program for my honors thesis. I really appreciate any help that can be provided.

I've pasted the error below:

`ERROR: test_is_output_correct_for_fishtaco_FDR_correction (main.FishTacoTestCase) Does FishTaco with FDR multiple hypothesis correction produce the correct output for

Traceback (most recent call last): File "test_fishtaco.py", line 570, in test_is_output_correct_for_fishtaco_FDR_correction with open("fishtaco_out_FDR_correction_STAT_run_log_SCORE_wilcoxon" FileNotFoundError: [Errno 2] No such file or directory: 'fishtaco_out_FDR_correction_STAT_run_log_SCORE_wilcoxon_ASSESSMENT_single_taxa.tab'

====================================================================== ERROR: test_is_output_correct_for_fishtaco_de_novo_inference (main.FishTacoTestCase) Does FishTaco with de novo inference produce the correct output

Traceback (most recent call last): File "test_fishtaco.py", line 342, in test_is_output_correct_for_fishtaco_de_novo_inference with open("fishtaco_out_de_novo_inf_STAT_run_log_SCORE_wilcoxon" FileNotFoundError: [Errno 2] No such file or directory: 'fishtaco_out_de_novo_inf_STAT_run_log_SCORE_wilcoxon_ASSESSMENT_single_taxa.tab'

====================================================================== ERROR: test_is_output_correct_for_fishtaco_filtering_by_function_list (main.FishTacoTestCase) Does FishTaco with filtering by function list produce the correct

Traceback (most recent call last): File "test_fishtaco.py", line 456, in test_is_output_correct_for_fishtaco_filtering_by_function_list with open("fishtaco_out_filtering_by_function_list_STAT_run_log_SCORE" FileNotFoundError: [Errno 2] No such file or directory: 'fishtaco_out_filtering_by_function_list_STAT_run_log_SCORE_wilcoxon_ASSESSMENT_single_taxa.tab'

====================================================================== ERROR: test_is_output_correct_for_fishtaco_no_inference (main.FishTacoTestCase) Does FishTaco with no inference produce the correct output for

Traceback (most recent call last): File "test_fishtaco.py", line 227, in test_is_output_correct_for_fishtaco_no_inference with open("fishtaco_out_no_inf_STAT_run_log_SCORE_wilcoxon" FileNotFoundError: [Errno 2] No such file or directory: 'fishtaco_out_no_inf_STAT_run_log_SCORE_wilcoxon_ASSESSMENT_single_taxa.tab'

====================================================================== ERROR: test_is_output_correct_for_fishtaco_predict_functional_profile (main.FishTacoTestCase) Does FishTaco with predicting the functional profiles produce the

Traceback (most recent call last): File "test_fishtaco.py", line 398, in test_is_output_correct_for_fishtaco_predict_functional_profile with open("fishtaco_out_predict_function_STAT_run_log_SCORE_wilcoxon" FileNotFoundError: [Errno 2] No such file or directory: 'fishtaco_out_predict_function_STAT_run_log_SCORE_wilcoxon_ASSESSMENT_single_taxa.tab'

====================================================================== ERROR: test_is_output_correct_for_fishtaco_prior_based_inference (main.FishTacoTestCase) Does FishTaco with prior-based inference produce the correct

Traceback (most recent call last): File "test_fishtaco.py", line 285, in test_is_output_correct_for_fishtaco_prior_based_inference with open("fishtaco_out_prior_based_inf_STAT_run_log_SCORE_wilcoxon" FileNotFoundError: [Errno 2] No such file or directory: 'fishtaco_out_prior_based_inf_STAT_run_log_SCORE_wilcoxon_ASSESSMENT_single_taxa.tab'

====================================================================== ERROR: test_is_output_correct_for_fishtaco_shapley_value (main.FishTacoTestCase) Does FishTaco with no inference produce the correct output for

Traceback (most recent call last): File "test_fishtaco.py", line 523, in test_is_output_correct_for_fishtaco_shapley_value test_output = pd.read_csv('fishtaco_outshapley' File "/home/aadeg/.local/lib/python3.8/site-packages/pandas/util/_decorators.py", line 311, in wrapper return func(*args, kwargs) File "/home/aadeg/.local/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 680, in read_csv return _read(filepath_or_buffer, kwds) File "/home/aadeg/.local/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 575, in _read parser = TextFileReader(filepath_or_buffer, kwds) File "/home/aadeg/.local/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 933, in init self._engine = self._make_engine(f, self.engine) File "/home/aadeg/.local/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 1217, in _make_engine self.handles = get_handle( # type: ignore[call-overload] File "/home/aadeg/.local/lib/python3.8/site-packages/pandas/io/common.py", line 789, in get_handle handle = open( FileNotFoundError: [Errno 2] No such file or directory: 'fishtaco_out_shapley_STAT_taxa_contributions_SCORE_wilcoxon_ASSESSMENT_multi_taxa.tab'

====================================================================== ERROR: test_is_output_correct_for_fishtaco_stricter_FDR_filter (main.FishTacoTestCase) Does FishTaco with a stricter FDR filter produce the correct output for

Traceback (most recent call last): File "test_fishtaco.py", line 630, in test_is_output_correct_for_fishtaco_stricter_FDR_filter with open("fishtaco_out_stricter_FDR_filter_STAT_run_log_SCORE_wilcoxon" FileNotFoundError: [Errno 2] No such file or directory: 'fishtaco_out_stricter_FDR_filter_STAT_run_log_SCORE_wilcoxon_ASSESSMENT_single_taxa.tab'

====================================================================== ERROR: test_learn_non_neg_elastic_net_de_novo (main.FishTacoTestCase) Does learn_non_neg_elastic_net_with_prior.py produce the correct

Traceback (most recent call last): File "test_fishtaco.py", line 182, in test_learn_non_neg_elastic_net_de_novo test_output = pd.read_csv('test_de_novo_based_inf_STAT_taxalearned' File "/home/aadeg/.local/lib/python3.8/site-packages/pandas/util/_decorators.py", line 311, in wrapper return func(*args, kwargs) File "/home/aadeg/.local/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 680, in read_csv return _read(filepath_or_buffer, kwds) File "/home/aadeg/.local/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 575, in _read parser = TextFileReader(filepath_or_buffer, kwds) File "/home/aadeg/.local/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 933, in init self._engine = self._make_engine(f, self.engine) File "/home/aadeg/.local/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 1217, in _make_engine self.handles = get_handle( # type: ignore[call-overload] File "/home/aadeg/.local/lib/python3.8/site-packages/pandas/io/common.py", line 789, in get_handle handle = open( FileNotFoundError: [Errno 2] No such file or directory: 'test_de_novo_based_inf_STAT_taxa_learned_copy_num_SCORE_wilcoxon_ASSESSMENT_single_taxa.tab'

====================================================================== ERROR: test_learn_non_neg_elastic_net_with_prior (main.FishTacoTestCase) Does learn_non_neg_elastic_net_with_prior.py produce the correct

Traceback (most recent call last): File "test_fishtaco.py", line 137, in test_learn_non_neg_elastic_net_with_prior test_output = pd.read_csv('test_prior_based_inf_STAT_taxalearned' File "/home/aadeg/.local/lib/python3.8/site-packages/pandas/util/_decorators.py", line 311, in wrapper return func(*args, kwargs) File "/home/aadeg/.local/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 680, in read_csv return _read(filepath_or_buffer, kwds) File "/home/aadeg/.local/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 575, in _read parser = TextFileReader(filepath_or_buffer, kwds) File "/home/aadeg/.local/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 933, in init self._engine = self._make_engine(f, self.engine) File "/home/aadeg/.local/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 1217, in _make_engine self.handles = get_handle( # type: ignore[call-overload] File "/home/aadeg/.local/lib/python3.8/site-packages/pandas/io/common.py", line 789, in get_handle handle = open( FileNotFoundError: [Errno 2] No such file or directory: 'test_prior_based_inf_STAT_taxa_learned_copy_num_SCORE_wilcoxon_ASSESSMENT_single_taxa.tab'

Ran 12 tests in 6.815s

FAILED (errors=10) `

engal commented 2 years ago

Hi! It looks like there's an issue finding the output files that should have been generated by FishTaco when the tests were run. Are you able to share all of the output generated by the test script? It looks like this may just be the errors, but the test script should have printed other messages as well while it was running. If nothing else was printed, then there may be other issues.

anitatiknaik commented 1 year ago

error while running test_fishtaco.py

============================================================== Testing compute_differential_abundance.py Path to examples:/root/anaconda3/lib/python3.9/site-packages/FishTaco-1.1.1-py3.9.egg/fishtaco

Given parameters: {'input_file': '/root/anaconda3/lib/python3.9/site-packages/FishTaco-1.1.1-py3.9.egg/fishtaco/examples/METAPHLAN_taxa_vs_SAMPLE_for_K00001.tab', 'class_file': '/root/anaconda3/lib/python3.9/site-packages/FishTaco-1.1.1-py3.9.egg/fishtaco/examples/SAMPLE_vs_CLASS.tab', 'class_header': True, 'row_metadata': None, 'output_file': 'test_compute_differential_abundance.tab', 'method': 'Wilcoxon', 'control_label': '0', 'case_label': '1', 'verbose': True} Loading files... Done. Number of samples: 213 Number of controls: 107 Number of cases: 106 Number of functions: 10 Computing differential abundance... Done. Writing output... Done. .============================================================== Testing compute_pathway_abundance.py Path to examples:/root/anaconda3/lib/python3.9/site-packages/FishTaco-1.1.1-py3.9.egg/fishtaco

Given parameters: {'ko_abun_file': '/root/anaconda3/lib/python3.9/site-packages/FishTaco-1.1.1-py3.9.egg/fishtaco/examples/KO_vs_SAMPLE_MUSiCC.tab', 'ko_to_pathway_file': '/root/anaconda3/lib/python3.9/site-packages/FishTaco-1.1.1-py3.9.egg/fishtaco/data/KOvsPATHWAY_BACTERIAL_KEGG_2013_07_15.tab', 'output_file': 'test_compute_pathway_abundance.tab', 'output_counts_file': 'test_compute_pathway_abundance_counts.tab', 'mapping_method': 'naive', 'compute_method': 'sum', 'transpose_ko_abundance': False, 'transpose_output': False, 'verbose': True} Reading files... Done. Writing output... Done. .============================================================== Testing compute_contribution_to_DA.py (de novo inference) Path to examples:/root/anaconda3/lib/python3.9/site-packages/FishTaco-1.1.1-py3.9.egg/fishtaco

Traceback (most recent call last): File "/root/anaconda3/bin/run_fishtaco.py", line 4, in import('pkg_resources').run_script('FishTaco==1.1.1', 'run_fishtaco.py') File "/root/anaconda3/lib/python3.9/site-packages/pkg_resources/init.py", line 651, in run_script self.require(requires)[0].run_script(script_name, ns) File "/root/anaconda3/lib/python3.9/site-packages/pkg_resources/init.py", line 1448, in run_script exec(code, namespace, namespace) File "/root/anaconda3/lib/python3.9/site-packages/FishTaco-1.1.1-py3.9.egg/EGG-INFO/scripts/run_fishtaco.py", line 12, in from fishtaco.compute_contribution_to_DA import main File "/root/anaconda3/lib/python3.9/site-packages/FishTaco-1.1.1-py3.9.egg/fishtaco/compute_contribution_to_DA.py", line 73, in from fishtaco import learn_non_neg_elastic_net_with_prior File "/root/anaconda3/lib/python3.9/site-packages/FishTaco-1.1.1-py3.9.egg/fishtaco/learn_non_neg_elastic_net_with_prior.py", line 25, in from sklearn import cross_validation, linear_model ImportError: cannot import name 'cross_validation' from 'sklearn' (/root/anaconda3/lib/python3.9/site-packages/sklearn/init.py) Testing output... E============================================================== Testing compute_contribution_to_DA.py (filter by list) Path to examples:/root/anaconda3/lib/python3.9/site-packages/FishTaco-1.1.1-py3.9.egg/fishtaco

Traceback (most recent call last): File "/root/anaconda3/bin/run_fishtaco.py", line 4, in import('pkg_resources').run_script('FishTaco==1.1.1', 'run_fishtaco.py') File "/root/anaconda3/lib/python3.9/site-packages/pkg_resources/init.py", line 651, in run_script self.require(requires)[0].run_script(script_name, ns) File "/root/anaconda3/lib/python3.9/site-packages/pkg_resources/init.py", line 1448, in run_script exec(code, namespace, namespace) File "/root/anaconda3/lib/python3.9/site-packages/FishTaco-1.1.1-py3.9.egg/EGG-INFO/scripts/run_fishtaco.py", line 12, in from fishtaco.compute_contribution_to_DA import main File "/root/anaconda3/lib/python3.9/site-packages/FishTaco-1.1.1-py3.9.egg/fishtaco/compute_contribution_to_DA.py", line 73, in from fishtaco import learn_non_neg_elastic_net_with_prior File "/root/anaconda3/lib/python3.9/site-packages/FishTaco-1.1.1-py3.9.egg/fishtaco/learn_non_neg_elastic_net_with_prior.py", line 25, in from sklearn import cross_validation, linear_model ImportError: cannot import name 'cross_validation' from 'sklearn' (/root/anaconda3/lib/python3.9/site-packages/sklearn/init.py) Testing output... E============================================================== Testing compute_contribution_to_DA.py (no inference) Path to examples:/root/anaconda3/lib/python3.9/site-packages/FishTaco-1.1.1-py3.9.egg/fishtaco

Traceback (most recent call last): File "/root/anaconda3/bin/run_fishtaco.py", line 4, in import('pkg_resources').run_script('FishTaco==1.1.1', 'run_fishtaco.py') File "/root/anaconda3/lib/python3.9/site-packages/pkg_resources/init.py", line 651, in run_script self.require(requires)[0].run_script(script_name, ns) File "/root/anaconda3/lib/python3.9/site-packages/pkg_resources/init.py", line 1448, in run_script exec(code, namespace, namespace) File "/root/anaconda3/lib/python3.9/site-packages/FishTaco-1.1.1-py3.9.egg/EGG-INFO/scripts/run_fishtaco.py", line 12, in from fishtaco.compute_contribution_to_DA import main File "/root/anaconda3/lib/python3.9/site-packages/FishTaco-1.1.1-py3.9.egg/fishtaco/compute_contribution_to_DA.py", line 73, in from fishtaco import learn_non_neg_elastic_net_with_prior File "/root/anaconda3/lib/python3.9/site-packages/FishTaco-1.1.1-py3.9.egg/fishtaco/learn_non_neg_elastic_net_with_prior.py", line 25, in from sklearn import cross_validation, linear_model ImportError: cannot import name 'cross_validation' from 'sklearn' (/root/anaconda3/lib/python3.9/site-packages/sklearn/init.py) Testing output... E============================================================== Testing compute_contribution_to_DA.py (predict function) Path to examples:/root/anaconda3/lib/python3.9/site-packages/FishTaco-1.1.1-py3.9.egg/fishtaco

Traceback (most recent call last): File "/root/anaconda3/bin/run_fishtaco.py", line 4, in import('pkg_resources').run_script('FishTaco==1.1.1', 'run_fishtaco.py') File "/root/anaconda3/lib/python3.9/site-packages/pkg_resources/init.py", line 651, in run_script self.require(requires)[0].run_script(script_name, ns) File "/root/anaconda3/lib/python3.9/site-packages/pkg_resources/init.py", line 1448, in run_script exec(code, namespace, namespace) File "/root/anaconda3/lib/python3.9/site-packages/FishTaco-1.1.1-py3.9.egg/EGG-INFO/scripts/run_fishtaco.py", line 12, in from fishtaco.compute_contribution_to_DA import main File "/root/anaconda3/lib/python3.9/site-packages/FishTaco-1.1.1-py3.9.egg/fishtaco/compute_contribution_to_DA.py", line 73, in from fishtaco import learn_non_neg_elastic_net_with_prior File "/root/anaconda3/lib/python3.9/site-packages/FishTaco-1.1.1-py3.9.egg/fishtaco/learn_non_neg_elastic_net_with_prior.py", line 25, in from sklearn import cross_validation, linear_model ImportError: cannot import name 'cross_validation' from 'sklearn' (/root/anaconda3/lib/python3.9/site-packages/sklearn/init.py) Testing output... E============================================================== Testing compute_contribution_to_DA.py (prior-based inference) Path to examples:/root/anaconda3/lib/python3.9/site-packages/FishTaco-1.1.1-py3.9.egg/fishtaco

Traceback (most recent call last): File "/root/anaconda3/bin/run_fishtaco.py", line 4, in import('pkg_resources').run_script('FishTaco==1.1.1', 'run_fishtaco.py') File "/root/anaconda3/lib/python3.9/site-packages/pkg_resources/init.py", line 651, in run_script self.require(requires)[0].run_script(script_name, ns) File "/root/anaconda3/lib/python3.9/site-packages/pkg_resources/init.py", line 1448, in run_script exec(code, namespace, namespace) File "/root/anaconda3/lib/python3.9/site-packages/FishTaco-1.1.1-py3.9.egg/EGG-INFO/scripts/run_fishtaco.py", line 12, in from fishtaco.compute_contribution_to_DA import main File "/root/anaconda3/lib/python3.9/site-packages/FishTaco-1.1.1-py3.9.egg/fishtaco/compute_contribution_to_DA.py", line 73, in from fishtaco import learn_non_neg_elastic_net_with_prior File "/root/anaconda3/lib/python3.9/site-packages/FishTaco-1.1.1-py3.9.egg/fishtaco/learn_non_neg_elastic_net_with_prior.py", line 25, in from sklearn import cross_validation, linear_model ImportError: cannot import name 'cross_validation' from 'sklearn' (/root/anaconda3/lib/python3.9/site-packages/sklearn/init.py) Testing output... E============================================================== Testing compute_contribution_to_DA.py (Shapley value) Path to examples:/root/anaconda3/lib/python3.9/site-packages/FishTaco-1.1.1-py3.9.egg/fishtaco

Traceback (most recent call last): File "/root/anaconda3/bin/run_fishtaco.py", line 4, in import('pkg_resources').run_script('FishTaco==1.1.1', 'run_fishtaco.py') File "/root/anaconda3/lib/python3.9/site-packages/pkg_resources/init.py", line 651, in run_script self.require(requires)[0].run_script(script_name, ns) File "/root/anaconda3/lib/python3.9/site-packages/pkg_resources/init.py", line 1448, in run_script exec(code, namespace, namespace) File "/root/anaconda3/lib/python3.9/site-packages/FishTaco-1.1.1-py3.9.egg/EGG-INFO/scripts/run_fishtaco.py", line 12, in from fishtaco.compute_contribution_to_DA import main File "/root/anaconda3/lib/python3.9/site-packages/FishTaco-1.1.1-py3.9.egg/fishtaco/compute_contribution_to_DA.py", line 73, in from fishtaco import learn_non_neg_elastic_net_with_prior File "/root/anaconda3/lib/python3.9/site-packages/FishTaco-1.1.1-py3.9.egg/fishtaco/learn_non_neg_elastic_net_with_prior.py", line 25, in from sklearn import cross_validation, linear_model ImportError: cannot import name 'cross_validation' from 'sklearn' (/root/anaconda3/lib/python3.9/site-packages/sklearn/init.py) Testing output... E============================================================== Testing learn_non_neg_elastic_net_with_prior.py (de-novo) Path to examples:/root/anaconda3/lib/python3.9/site-packages/FishTaco-1.1.1-py3.9.egg/fishtaco

Traceback (most recent call last): File "/root/anaconda3/bin/run_fishtaco.py", line 4, in import('pkg_resources').run_script('FishTaco==1.1.1', 'run_fishtaco.py') File "/root/anaconda3/lib/python3.9/site-packages/pkg_resources/init.py", line 651, in run_script self.require(requires)[0].run_script(script_name, ns) File "/root/anaconda3/lib/python3.9/site-packages/pkg_resources/init.py", line 1448, in run_script exec(code, namespace, namespace) File "/root/anaconda3/lib/python3.9/site-packages/FishTaco-1.1.1-py3.9.egg/EGG-INFO/scripts/run_fishtaco.py", line 12, in from fishtaco.compute_contribution_to_DA import main File "/root/anaconda3/lib/python3.9/site-packages/FishTaco-1.1.1-py3.9.egg/fishtaco/compute_contribution_to_DA.py", line 73, in from fishtaco import learn_non_neg_elastic_net_with_prior File "/root/anaconda3/lib/python3.9/site-packages/FishTaco-1.1.1-py3.9.egg/fishtaco/learn_non_neg_elastic_net_with_prior.py", line 25, in from sklearn import cross_validation, linear_model ImportError: cannot import name 'cross_validation' from 'sklearn' (/root/anaconda3/lib/python3.9/site-packages/sklearn/init.py) E============================================================== Testing learn_non_neg_elastic_net_with_prior.py (prior-based) Path to examples:/root/anaconda3/lib/python3.9/site-packages/FishTaco-1.1.1-py3.9.egg/fishtaco

Traceback (most recent call last): File "/root/anaconda3/bin/run_fishtaco.py", line 4, in import('pkg_resources').run_script('FishTaco==1.1.1', 'run_fishtaco.py') File "/root/anaconda3/lib/python3.9/site-packages/pkg_resources/init.py", line 651, in run_script self.require(requires)[0].run_script(script_name, ns) File "/root/anaconda3/lib/python3.9/site-packages/pkg_resources/init.py", line 1448, in run_script exec(code, namespace, namespace) File "/root/anaconda3/lib/python3.9/site-packages/FishTaco-1.1.1-py3.9.egg/EGG-INFO/scripts/run_fishtaco.py", line 12, in from fishtaco.compute_contribution_to_DA import main File "/root/anaconda3/lib/python3.9/site-packages/FishTaco-1.1.1-py3.9.egg/fishtaco/compute_contribution_to_DA.py", line 73, in from fishtaco import learn_non_neg_elastic_net_with_prior File "/root/anaconda3/lib/python3.9/site-packages/FishTaco-1.1.1-py3.9.egg/fishtaco/learn_non_neg_elastic_net_with_prior.py", line 25, in from sklearn import cross_validation, linear_model ImportError: cannot import name 'cross_validation' from 'sklearn' (/root/anaconda3/lib/python3.9/site-packages/sklearn/init.py) E

ERROR: test_is_output_correct_for_fishtaco_de_novo_inference (main.FishTacoTestCase) Does FishTaco with de novo inference produce the correct output

Traceback (most recent call last): File "/root/anaconda3/lib/python3.9/site-packages/FishTaco-1.1.1-py3.9.egg/EGG-INFO/scripts/test_fishtaco.py", line 342, in test_is_output_correct_for_fishtaco_de_novo_inference with open("fishtaco_out_de_novo_inf_STAT_run_log_SCORE_wilcoxon" FileNotFoundError: [Errno 2] No such file or directory: 'fishtaco_out_de_novo_inf_STAT_run_log_SCORE_wilcoxon_ASSESSMENT_single_taxa.tab'

====================================================================== ERROR: test_is_output_correct_for_fishtaco_filtering_by_function_list (main.FishTacoTestCase) Does FishTaco with filtering by function list produce the correct

Traceback (most recent call last): File "/root/anaconda3/lib/python3.9/site-packages/FishTaco-1.1.1-py3.9.egg/EGG-INFO/scripts/test_fishtaco.py", line 456, in test_is_output_correct_for_fishtaco_filtering_by_function_list with open("fishtaco_out_filtering_by_function_list_STAT_run_log_SCORE" FileNotFoundError: [Errno 2] No such file or directory: 'fishtaco_out_filtering_by_function_list_STAT_run_log_SCORE_wilcoxon_ASSESSMENT_single_taxa.tab'

====================================================================== ERROR: test_is_output_correct_for_fishtaco_no_inference (main.FishTacoTestCase) Does FishTaco with no inference produce the correct output for

Traceback (most recent call last): File "/root/anaconda3/lib/python3.9/site-packages/FishTaco-1.1.1-py3.9.egg/EGG-INFO/scripts/test_fishtaco.py", line 227, in test_is_output_correct_for_fishtaco_no_inference with open("fishtaco_out_no_inf_STAT_run_log_SCORE_wilcoxon" FileNotFoundError: [Errno 2] No such file or directory: 'fishtaco_out_no_inf_STAT_run_log_SCORE_wilcoxon_ASSESSMENT_single_taxa.tab'

====================================================================== ERROR: test_is_output_correct_for_fishtaco_predict_functional_profile (main.FishTacoTestCase) Does FishTaco with predicting the functional profiles produce the

Traceback (most recent call last): File "/root/anaconda3/lib/python3.9/site-packages/FishTaco-1.1.1-py3.9.egg/EGG-INFO/scripts/test_fishtaco.py", line 398, in test_is_output_correct_for_fishtaco_predict_functional_profile with open("fishtaco_out_predict_function_STAT_run_log_SCORE_wilcoxon" FileNotFoundError: [Errno 2] No such file or directory: 'fishtaco_out_predict_function_STAT_run_log_SCORE_wilcoxon_ASSESSMENT_single_taxa.tab'

====================================================================== ERROR: test_is_output_correct_for_fishtaco_prior_based_inference (main.FishTacoTestCase) Does FishTaco with prior-based inference produce the correct

Traceback (most recent call last): File "/root/anaconda3/lib/python3.9/site-packages/FishTaco-1.1.1-py3.9.egg/EGG-INFO/scripts/test_fishtaco.py", line 285, in test_is_output_correct_for_fishtaco_prior_based_inference with open("fishtaco_out_prior_based_inf_STAT_run_log_SCORE_wilcoxon" FileNotFoundError: [Errno 2] No such file or directory: 'fishtaco_out_prior_based_inf_STAT_run_log_SCORE_wilcoxon_ASSESSMENT_single_taxa.tab'

====================================================================== ERROR: test_is_output_correct_for_fishtaco_shapley_value (main.FishTacoTestCase) Does FishTaco with no inference produce the correct output for

Traceback (most recent call last): File "/root/anaconda3/lib/python3.9/site-packages/FishTaco-1.1.1-py3.9.egg/EGG-INFO/scripts/test_fishtaco.py", line 523, in test_is_output_correct_for_fishtaco_shapley_value test_output = pd.read_csv('fishtaco_outshapley' File "/root/anaconda3/lib/python3.9/site-packages/pandas/util/_decorators.py", line 311, in wrapper return func(*args, kwargs) File "/root/anaconda3/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 680, in read_csv return _read(filepath_or_buffer, kwds) File "/root/anaconda3/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 575, in _read parser = TextFileReader(filepath_or_buffer, kwds) File "/root/anaconda3/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 933, in init self._engine = self._make_engine(f, self.engine) File "/root/anaconda3/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1217, in _make_engine self.handles = get_handle( # type: ignore[call-overload] File "/root/anaconda3/lib/python3.9/site-packages/pandas/io/common.py", line 789, in get_handle handle = open( FileNotFoundError: [Errno 2] No such file or directory: 'fishtaco_out_shapley_STAT_taxa_contributions_SCORE_wilcoxon_ASSESSMENT_multi_taxa.tab'

====================================================================== ERROR: test_learn_non_neg_elastic_net_de_novo (main.FishTacoTestCase) Does learn_non_neg_elastic_net_with_prior.py produce the correct

Traceback (most recent call last): File "/root/anaconda3/lib/python3.9/site-packages/FishTaco-1.1.1-py3.9.egg/EGG-INFO/scripts/test_fishtaco.py", line 182, in test_learn_non_neg_elastic_net_de_novo test_output = pd.read_csv('test_de_novo_based_inf_STAT_taxalearned' File "/root/anaconda3/lib/python3.9/site-packages/pandas/util/_decorators.py", line 311, in wrapper return func(*args, kwargs) File "/root/anaconda3/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 680, in read_csv return _read(filepath_or_buffer, kwds) File "/root/anaconda3/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 575, in _read parser = TextFileReader(filepath_or_buffer, kwds) File "/root/anaconda3/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 933, in init self._engine = self._make_engine(f, self.engine) File "/root/anaconda3/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1217, in _make_engine self.handles = get_handle( # type: ignore[call-overload] File "/root/anaconda3/lib/python3.9/site-packages/pandas/io/common.py", line 789, in get_handle handle = open( FileNotFoundError: [Errno 2] No such file or directory: 'test_de_novo_based_inf_STAT_taxa_learned_copy_num_SCORE_wilcoxon_ASSESSMENT_single_taxa.tab'

====================================================================== ERROR: test_learn_non_neg_elastic_net_with_prior (main.FishTacoTestCase) Does learn_non_neg_elastic_net_with_prior.py produce the correct

Traceback (most recent call last): File "/root/anaconda3/lib/python3.9/site-packages/FishTaco-1.1.1-py3.9.egg/EGG-INFO/scripts/test_fishtaco.py", line 137, in test_learn_non_neg_elastic_net_with_prior test_output = pd.read_csv('test_prior_based_inf_STAT_taxalearned' File "/root/anaconda3/lib/python3.9/site-packages/pandas/util/_decorators.py", line 311, in wrapper return func(*args, kwargs) File "/root/anaconda3/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 680, in read_csv return _read(filepath_or_buffer, kwds) File "/root/anaconda3/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 575, in _read parser = TextFileReader(filepath_or_buffer, kwds) File "/root/anaconda3/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 933, in init self._engine = self._make_engine(f, self.engine) File "/root/anaconda3/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1217, in _make_engine self.handles = get_handle( # type: ignore[call-overload] File "/root/anaconda3/lib/python3.9/site-packages/pandas/io/common.py", line 789, in get_handle handle = open( FileNotFoundError: [Errno 2] No such file or directory: 'test_prior_based_inf_STAT_taxa_learned_copy_num_SCORE_wilcoxon_ASSESSMENT_single_taxa.tab'

Ran 10 tests in 13.070s

FAILED (errors=8)