DianaSpurite commented 1 year ago

Pull Request

This PR is for a

[x] New Publication(s)
[ ] Correction

For the following list(s):

[ ] ancientmetagenome-environmental (README)
[ ] ancientmetagenome-hostassociated (README)
[x] ancientsinglegenome-hostassociated (README)

New Publication

Publication Information

This pull request is to add samples from the following publication(s): https://doi.org/10.1098/rspb.2023.0622)

This is to close #1096

Checklist

[x] Publication is published (preprints currently not accepted)?
[x] Checked the publication is not already in the database?
[x] Checked samples in this publication are not previously published data (newly re-sequenced metagenomes are OK!)?
[x] Samples are shotgun metagenomes (hostassociated-singlegenome may also contain whole-genome enriched data)?
[x] Checked the list follows conventions as described in the corresponding sample type's README file (e.g. using ERS/SRS accession codes for ENA/SRA)?
[x] Changelog is updated to include the publication under 'Added'?
[ ] Pull request has passed validation checks (see automated comment from github-bot)?
[ ] Review requested from @SPAAM-community/ancientmetagenomedir?
[x] (If applicable) Made a separate PR to add new categories to controlled lists (stored under /assets/enums, e.g. material or archive)? If so the corresponding PR is here:

github-actions[bot] commented 1 year ago

AMDirT, version 1.4.6

Samples

Ancient Metagenome Host Associated

Traceback (most recent call last): File "/opt/hostedtoolcache/Python/3.9.17/x64/bin/AMDirT", line 8, in sys.exit(cli()) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 1157, in call return self.main(args, kwargs) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 1078, in main rv = self.invoke(ctx) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 1688, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 1434, in invoke return ctx.invoke(self.callback, ctx.params) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 783, in invoke return __callback(args, *kwargs) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/decorators.py", line 33, in new_func return f(get_current_context(), args, kwargs) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/AMDirT/cli.py", line 78, in validate run_validation(kwargs, **ctx.obj) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/AMDirT/validate/init.py", line 21, in run_validation v.validate_schema() File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/AMDirT/validate/domain/init.py", line 235, in validate_schema for err in validator.iter_errors(self.dataset_json): File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 363, in iter_errors for error in errors: File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/_legacy_validators.py", line 115, in items_draft6_draft7_draft201909 yield from validator.descend(item, items, path=index) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 411, in descend for error in errors: File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/_validators.py", line 305, in properties yield from validator.descend( File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 411, in descend for error in errors: File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/_validators.py", line 284, in ref yield from validator._validate_reference(ref=ref, instance=instance) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 441, in _validate_reference resolved = self._resolver.lookup(ref) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/referencing/_core.py", line 586, in lookup retrieved = self._registry.get_or_retrieve(uri) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/referencing/_core.py", line 336, in get_or_retrieve resource = registry._retrieve(uri) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 120, in _warn_for_remote_retrieve return referencing.Resource.from_contents(json.load(response)) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/referencing/_core.py", line 129, in from_contents raise exceptions.CannotDetermineSpecification(contents) referencing.exceptions.CannotDetermineSpecification: {'enum': ['Afghanistan', 'Albania', 'Algeria', 'American Samoa', 'Andorra', 'Angola', 'Anguilla', 'Antarctica', 'Antigua and Barbuda', 'Arctic Ocean', 'Argentina', 'Armenia', 'Aruba', 'Ashmore and Cartier Islands', 'Atlantic Ocean', 'Australia', 'Austria', 'Azerbaijan', 'Bahamas', 'Bahrain', 'Baltic Sea', 'Baker Island', 'Bangladesh', 'Barbados', 'Bassas da India', 'Belarus', 'Belgium', 'Belize', 'Benin', 'Bermuda', 'Bhutan', 'Bolivia', 'Borneo', 'Bosnia and Herzegovina', 'Botswana', 'Bouvet Island', 'Brazil', 'British Virgin Islands', 'Brunei', 'Bulgaria', 'Burkina Faso', 'Burundi', 'Cambodia', 'Cameroon', 'Canada', 'Cape Verde', 'Cayman Islands', 'Central African Republic', 'Chad', 'Chile', 'China', 'Christmas Island', 'Clipperton Island', 'Cocos Islands', 'Colombia', 'Comoros', 'Cook Islands', 'Coral Sea Islands', 'Costa Rica', "Cote d'Ivoire", 'Croatia', 'Cuba', 'Curacao', 'Cyprus', 'Czech Republic', 'Democratic Republic of the Congo', 'Denmark', 'Djibouti', 'Dominica', 'Dominican Republic', 'Ecuador', 'Egypt', 'El Salvador', 'Equatorial Guinea', 'Eritrea', 'Estonia', 'Eswatini', 'Ethiopia', 'Europa Island', 'Falkland Islands (Islas Malvinas)', 'Faroe Islands', 'Fiji', 'Finland', 'France', 'French Guiana', 'French Polynesia', 'French Southern and Antarctic Lands', 'Gabon', 'Gambia', 'Gaza Strip', 'Georgia', 'Germany', 'Ghana', 'Gibraltar', 'Glorioso Islands', 'Greece', 'Greenland', 'Grenada', 'Guadeloupe', 'Guam', 'Guatemala', 'Guernsey', 'Guinea', 'Guinea-Bissau', 'Guyana', 'Haiti', 'Heard Island and McDonald Islands', 'Honduras', 'Hong Kong', 'Howland Island', 'Hungary', 'Iceland', 'India', 'Indian Ocean', 'Indonesia', 'Iran', 'Iraq', 'Ireland', 'Isle of Man', 'Israel', 'Italy', 'Jamaica', 'Jan Mayen', 'Japan', 'Jarvis Island', 'Jersey', 'Johnston Atoll', 'Jordan', 'Juan de Nova Island', 'Kazakhstan', 'Kenya', 'Kerguelen Archipelago', 'Kingman Reef', 'Kiribati', 'Kosovo', 'Kuwait', 'Kyrgyzstan', 'Laos', 'Latvia', 'Lebanon', 'Lesotho', 'Liberia', 'Libya', 'Liechtenstein', 'Line Islands', 'Lithuania', 'Luxembourg', 'Macau', 'Madagascar', 'Malawi', 'Malaysia', 'Maldives', 'Mali', 'Malta', 'Marshall Islands', 'Martinique', 'Mauritania', 'Mauritius', 'Mayotte', 'Mediterranean Sea', 'Mexico', 'Micronesia', 'Midway Islands', 'Moldova', 'Monaco', 'Mongolia', 'Montenegro', 'Montserrat', 'Morocco', 'Mozambique', 'Myanmar', 'Namibia', 'Nauru', 'Navassa Island', 'Nepal', 'Netherlands', 'New Caledonia', 'New Zealand', 'Nicaragua', 'Niger', 'Nigeria', 'Niue', 'Norfolk Island', 'North Korea', 'North Macedonia', 'North Sea', 'Northern Mariana Islands', 'Norway', 'Oman', 'Pacific Ocean', 'Pakistan', 'Palau', 'Palmyra Atoll', 'Panama', 'Papua New Guinea', 'Paracel Islands', 'Paraguay', 'Peru', 'Philippines', 'Pitcairn Islands', 'Poland', 'Portugal', 'Puerto Rico', 'Qatar', 'Republic of the Congo', 'Reunion', 'Romania', 'Ross Sea', 'Russia', 'Rwanda', 'Saint Helena', 'Saint Kitts and Nevis', 'Saint Lucia', 'Saint Pierre and Miquelon', 'Saint Vincent and the Grenadines', 'Samoa', 'San Marino', 'Sao Tome and Principe', 'Saudi Arabia', 'Senegal', 'Serbia', 'Seychelles', 'Sierra Leone', 'Singapore', 'Sint Maarten', 'Slovakia', 'Slovenia', 'Solomon Islands', 'Somalia', 'South Africa', 'South Georgia and the South Sandwich Islands', 'South Korea', 'South Sudan', 'Southern Ocean', 'Spain', 'Spratly Islands', 'Sri Lanka', 'State of Palestine', 'Sudan', 'Suriname', 'Svalbard', 'Sweden', 'Switzerland', 'Syria', 'Taiwan', 'Tajikistan', 'Tanzania', 'Tasman Sea', 'Thailand', 'Timor-Leste', 'Togo', 'Tokelau', 'Tonga', 'Trinidad and Tobago', 'Tromelin Island', 'Tunisia', 'Turkey', 'Turkmenistan', 'Turks and Caicos Islands', 'Tuvalu', 'USA', 'Uganda', 'Ukraine', 'United Arab Emirates', 'United Kingdom', 'Uruguay', 'Uzbekistan', 'Vanuatu', 'Venezuela', 'Viet Nam', 'Virgin Islands', 'Wake Island', 'Wallis and Futuna', 'West Bank', 'Western Sahara', 'Yemen', 'Zambia', 'Zimbabwe', 'Unknown']}

Ancient Single Genome Host Associated

Traceback (most recent call last): File "/opt/hostedtoolcache/Python/3.9.17/x64/bin/AMDirT", line 8, in sys.exit(cli()) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 1157, in call return self.main(args, kwargs) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 1078, in main rv = self.invoke(ctx) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 1688, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 1434, in invoke return ctx.invoke(self.callback, ctx.params) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 783, in invoke return __callback(args, *kwargs) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/decorators.py", line 33, in new_func return f(get_current_context(), args, kwargs) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/AMDirT/cli.py", line 78, in validate run_validation(kwargs, **ctx.obj) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/AMDirT/validate/init.py", line 21, in run_validation v.validate_schema() File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/AMDirT/validate/domain/init.py", line 235, in validate_schema for err in validator.iter_errors(self.dataset_json): File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 363, in iter_errors for error in errors: File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/_legacy_validators.py", line 115, in items_draft6_draft7_draft201909 yield from validator.descend(item, items, path=index) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 411, in descend for error in errors: File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/_validators.py", line 305, in properties yield from validator.descend( File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 411, in descend for error in errors: File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/_validators.py", line 284, in ref yield from validator._validate_reference(ref=ref, instance=instance) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 441, in _validate_reference resolved = self._resolver.lookup(ref) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/referencing/_core.py", line 586, in lookup retrieved = self._registry.get_or_retrieve(uri) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/referencing/_core.py", line 336, in get_or_retrieve resource = registry._retrieve(uri) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 120, in _warn_for_remote_retrieve return referencing.Resource.from_contents(json.load(response)) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/referencing/_core.py", line 129, in from_contents raise exceptions.CannotDetermineSpecification(contents) referencing.exceptions.CannotDetermineSpecification: {'enum': ['Afghanistan', 'Albania', 'Algeria', 'American Samoa', 'Andorra', 'Angola', 'Anguilla', 'Antarctica', 'Antigua and Barbuda', 'Arctic Ocean', 'Argentina', 'Armenia', 'Aruba', 'Ashmore and Cartier Islands', 'Atlantic Ocean', 'Australia', 'Austria', 'Azerbaijan', 'Bahamas', 'Bahrain', 'Baltic Sea', 'Baker Island', 'Bangladesh', 'Barbados', 'Bassas da India', 'Belarus', 'Belgium', 'Belize', 'Benin', 'Bermuda', 'Bhutan', 'Bolivia', 'Borneo', 'Bosnia and Herzegovina', 'Botswana', 'Bouvet Island', 'Brazil', 'British Virgin Islands', 'Brunei', 'Bulgaria', 'Burkina Faso', 'Burundi', 'Cambodia', 'Cameroon', 'Canada', 'Cape Verde', 'Cayman Islands', 'Central African Republic', 'Chad', 'Chile', 'China', 'Christmas Island', 'Clipperton Island', 'Cocos Islands', 'Colombia', 'Comoros', 'Cook Islands', 'Coral Sea Islands', 'Costa Rica', "Cote d'Ivoire", 'Croatia', 'Cuba', 'Curacao', 'Cyprus', 'Czech Republic', 'Democratic Republic of the Congo', 'Denmark', 'Djibouti', 'Dominica', 'Dominican Republic', 'Ecuador', 'Egypt', 'El Salvador', 'Equatorial Guinea', 'Eritrea', 'Estonia', 'Eswatini', 'Ethiopia', 'Europa Island', 'Falkland Islands (Islas Malvinas)', 'Faroe Islands', 'Fiji', 'Finland', 'France', 'French Guiana', 'French Polynesia', 'French Southern and Antarctic Lands', 'Gabon', 'Gambia', 'Gaza Strip', 'Georgia', 'Germany', 'Ghana', 'Gibraltar', 'Glorioso Islands', 'Greece', 'Greenland', 'Grenada', 'Guadeloupe', 'Guam', 'Guatemala', 'Guernsey', 'Guinea', 'Guinea-Bissau', 'Guyana', 'Haiti', 'Heard Island and McDonald Islands', 'Honduras', 'Hong Kong', 'Howland Island', 'Hungary', 'Iceland', 'India', 'Indian Ocean', 'Indonesia', 'Iran', 'Iraq', 'Ireland', 'Isle of Man', 'Israel', 'Italy', 'Jamaica', 'Jan Mayen', 'Japan', 'Jarvis Island', 'Jersey', 'Johnston Atoll', 'Jordan', 'Juan de Nova Island', 'Kazakhstan', 'Kenya', 'Kerguelen Archipelago', 'Kingman Reef', 'Kiribati', 'Kosovo', 'Kuwait', 'Kyrgyzstan', 'Laos', 'Latvia', 'Lebanon', 'Lesotho', 'Liberia', 'Libya', 'Liechtenstein', 'Line Islands', 'Lithuania', 'Luxembourg', 'Macau', 'Madagascar', 'Malawi', 'Malaysia', 'Maldives', 'Mali', 'Malta', 'Marshall Islands', 'Martinique', 'Mauritania', 'Mauritius', 'Mayotte', 'Mediterranean Sea', 'Mexico', 'Micronesia', 'Midway Islands', 'Moldova', 'Monaco', 'Mongolia', 'Montenegro', 'Montserrat', 'Morocco', 'Mozambique', 'Myanmar', 'Namibia', 'Nauru', 'Navassa Island', 'Nepal', 'Netherlands', 'New Caledonia', 'New Zealand', 'Nicaragua', 'Niger', 'Nigeria', 'Niue', 'Norfolk Island', 'North Korea', 'North Macedonia', 'North Sea', 'Northern Mariana Islands', 'Norway', 'Oman', 'Pacific Ocean', 'Pakistan', 'Palau', 'Palmyra Atoll', 'Panama', 'Papua New Guinea', 'Paracel Islands', 'Paraguay', 'Peru', 'Philippines', 'Pitcairn Islands', 'Poland', 'Portugal', 'Puerto Rico', 'Qatar', 'Republic of the Congo', 'Reunion', 'Romania', 'Ross Sea', 'Russia', 'Rwanda', 'Saint Helena', 'Saint Kitts and Nevis', 'Saint Lucia', 'Saint Pierre and Miquelon', 'Saint Vincent and the Grenadines', 'Samoa', 'San Marino', 'Sao Tome and Principe', 'Saudi Arabia', 'Senegal', 'Serbia', 'Seychelles', 'Sierra Leone', 'Singapore', 'Sint Maarten', 'Slovakia', 'Slovenia', 'Solomon Islands', 'Somalia', 'South Africa', 'South Georgia and the South Sandwich Islands', 'South Korea', 'South Sudan', 'Southern Ocean', 'Spain', 'Spratly Islands', 'Sri Lanka', 'State of Palestine', 'Sudan', 'Suriname', 'Svalbard', 'Sweden', 'Switzerland', 'Syria', 'Taiwan', 'Tajikistan', 'Tanzania', 'Tasman Sea', 'Thailand', 'Timor-Leste', 'Togo', 'Tokelau', 'Tonga', 'Trinidad and Tobago', 'Tromelin Island', 'Tunisia', 'Turkey', 'Turkmenistan', 'Turks and Caicos Islands', 'Tuvalu', 'USA', 'Uganda', 'Ukraine', 'United Arab Emirates', 'United Kingdom', 'Uruguay', 'Uzbekistan', 'Vanuatu', 'Venezuela', 'Viet Nam', 'Virgin Islands', 'Wake Island', 'Wallis and Futuna', 'West Bank', 'Western Sahara', 'Yemen', 'Zambia', 'Zimbabwe', 'Unknown']}

Ancient Metagenome Environmental

Traceback (most recent call last): File "/opt/hostedtoolcache/Python/3.9.17/x64/bin/AMDirT", line 8, in sys.exit(cli()) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 1157, in call return self.main(args, kwargs) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 1078, in main rv = self.invoke(ctx) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 1688, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 1434, in invoke return ctx.invoke(self.callback, ctx.params) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 783, in invoke return __callback(args, *kwargs) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/decorators.py", line 33, in new_func return f(get_current_context(), args, kwargs) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/AMDirT/cli.py", line 78, in validate run_validation(kwargs, **ctx.obj) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/AMDirT/validate/init.py", line 21, in run_validation v.validate_schema() File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/AMDirT/validate/domain/init.py", line 235, in validate_schema for err in validator.iter_errors(self.dataset_json): File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 363, in iter_errors for error in errors: File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/_legacy_validators.py", line 115, in items_draft6_draft7_draft201909 yield from validator.descend(item, items, path=index) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 411, in descend for error in errors: File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/_validators.py", line 305, in properties yield from validator.descend( File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 411, in descend for error in errors: File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/_validators.py", line 284, in ref yield from validator._validate_reference(ref=ref, instance=instance) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 441, in _validate_reference resolved = self._resolver.lookup(ref) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/referencing/_core.py", line 586, in lookup retrieved = self._registry.get_or_retrieve(uri) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/referencing/_core.py", line 336, in get_or_retrieve resource = registry._retrieve(uri) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 120, in _warn_for_remote_retrieve return referencing.Resource.from_contents(json.load(response)) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/referencing/_core.py", line 129, in from_contents raise exceptions.CannotDetermineSpecification(contents) referencing.exceptions.CannotDetermineSpecification: {'enum': ['Afghanistan', 'Albania', 'Algeria', 'American Samoa', 'Andorra', 'Angola', 'Anguilla', 'Antarctica', 'Antigua and Barbuda', 'Arctic Ocean', 'Argentina', 'Armenia', 'Aruba', 'Ashmore and Cartier Islands', 'Atlantic Ocean', 'Australia', 'Austria', 'Azerbaijan', 'Bahamas', 'Bahrain', 'Baltic Sea', 'Baker Island', 'Bangladesh', 'Barbados', 'Bassas da India', 'Belarus', 'Belgium', 'Belize', 'Benin', 'Bermuda', 'Bhutan', 'Bolivia', 'Borneo', 'Bosnia and Herzegovina', 'Botswana', 'Bouvet Island', 'Brazil', 'British Virgin Islands', 'Brunei', 'Bulgaria', 'Burkina Faso', 'Burundi', 'Cambodia', 'Cameroon', 'Canada', 'Cape Verde', 'Cayman Islands', 'Central African Republic', 'Chad', 'Chile', 'China', 'Christmas Island', 'Clipperton Island', 'Cocos Islands', 'Colombia', 'Comoros', 'Cook Islands', 'Coral Sea Islands', 'Costa Rica', "Cote d'Ivoire", 'Croatia', 'Cuba', 'Curacao', 'Cyprus', 'Czech Republic', 'Democratic Republic of the Congo', 'Denmark', 'Djibouti', 'Dominica', 'Dominican Republic', 'Ecuador', 'Egypt', 'El Salvador', 'Equatorial Guinea', 'Eritrea', 'Estonia', 'Eswatini', 'Ethiopia', 'Europa Island', 'Falkland Islands (Islas Malvinas)', 'Faroe Islands', 'Fiji', 'Finland', 'France', 'French Guiana', 'French Polynesia', 'French Southern and Antarctic Lands', 'Gabon', 'Gambia', 'Gaza Strip', 'Georgia', 'Germany', 'Ghana', 'Gibraltar', 'Glorioso Islands', 'Greece', 'Greenland', 'Grenada', 'Guadeloupe', 'Guam', 'Guatemala', 'Guernsey', 'Guinea', 'Guinea-Bissau', 'Guyana', 'Haiti', 'Heard Island and McDonald Islands', 'Honduras', 'Hong Kong', 'Howland Island', 'Hungary', 'Iceland', 'India', 'Indian Ocean', 'Indonesia', 'Iran', 'Iraq', 'Ireland', 'Isle of Man', 'Israel', 'Italy', 'Jamaica', 'Jan Mayen', 'Japan', 'Jarvis Island', 'Jersey', 'Johnston Atoll', 'Jordan', 'Juan de Nova Island', 'Kazakhstan', 'Kenya', 'Kerguelen Archipelago', 'Kingman Reef', 'Kiribati', 'Kosovo', 'Kuwait', 'Kyrgyzstan', 'Laos', 'Latvia', 'Lebanon', 'Lesotho', 'Liberia', 'Libya', 'Liechtenstein', 'Line Islands', 'Lithuania', 'Luxembourg', 'Macau', 'Madagascar', 'Malawi', 'Malaysia', 'Maldives', 'Mali', 'Malta', 'Marshall Islands', 'Martinique', 'Mauritania', 'Mauritius', 'Mayotte', 'Mediterranean Sea', 'Mexico', 'Micronesia', 'Midway Islands', 'Moldova', 'Monaco', 'Mongolia', 'Montenegro', 'Montserrat', 'Morocco', 'Mozambique', 'Myanmar', 'Namibia', 'Nauru', 'Navassa Island', 'Nepal', 'Netherlands', 'New Caledonia', 'New Zealand', 'Nicaragua', 'Niger', 'Nigeria', 'Niue', 'Norfolk Island', 'North Korea', 'North Macedonia', 'North Sea', 'Northern Mariana Islands', 'Norway', 'Oman', 'Pacific Ocean', 'Pakistan', 'Palau', 'Palmyra Atoll', 'Panama', 'Papua New Guinea', 'Paracel Islands', 'Paraguay', 'Peru', 'Philippines', 'Pitcairn Islands', 'Poland', 'Portugal', 'Puerto Rico', 'Qatar', 'Republic of the Congo', 'Reunion', 'Romania', 'Ross Sea', 'Russia', 'Rwanda', 'Saint Helena', 'Saint Kitts and Nevis', 'Saint Lucia', 'Saint Pierre and Miquelon', 'Saint Vincent and the Grenadines', 'Samoa', 'San Marino', 'Sao Tome and Principe', 'Saudi Arabia', 'Senegal', 'Serbia', 'Seychelles', 'Sierra Leone', 'Singapore', 'Sint Maarten', 'Slovakia', 'Slovenia', 'Solomon Islands', 'Somalia', 'South Africa', 'South Georgia and the South Sandwich Islands', 'South Korea', 'South Sudan', 'Southern Ocean', 'Spain', 'Spratly Islands', 'Sri Lanka', 'State of Palestine', 'Sudan', 'Suriname', 'Svalbard', 'Sweden', 'Switzerland', 'Syria', 'Taiwan', 'Tajikistan', 'Tanzania', 'Tasman Sea', 'Thailand', 'Timor-Leste', 'Togo', 'Tokelau', 'Tonga', 'Trinidad and Tobago', 'Tromelin Island', 'Tunisia', 'Turkey', 'Turkmenistan', 'Turks and Caicos Islands', 'Tuvalu', 'USA', 'Uganda', 'Ukraine', 'United Arab Emirates', 'United Kingdom', 'Uruguay', 'Uzbekistan', 'Vanuatu', 'Venezuela', 'Viet Nam', 'Virgin Islands', 'Wake Island', 'Wallis and Futuna', 'West Bank', 'Western Sahara', 'Yemen', 'Zambia', 'Zimbabwe', 'Unknown']}

Libraries

Ancient Metagenome Host Associated

Traceback (most recent call last): File "/opt/hostedtoolcache/Python/3.9.17/x64/bin/AMDirT", line 8, in sys.exit(cli()) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 1157, in call return self.main(args, kwargs) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 1078, in main rv = self.invoke(ctx) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 1688, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 1434, in invoke return ctx.invoke(self.callback, ctx.params) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 783, in invoke return __callback(args, *kwargs) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/decorators.py", line 33, in new_func return f(get_current_context(), args, kwargs) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/AMDirT/cli.py", line 78, in validate run_validation(kwargs, **ctx.obj) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/AMDirT/validate/init.py", line 21, in run_validation v.validate_schema() File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/AMDirT/validate/domain/init.py", line 235, in validate_schema for err in validator.iter_errors(self.dataset_json): File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 363, in iter_errors for error in errors: File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/_legacy_validators.py", line 115, in items_draft6_draft7_draft201909 yield from validator.descend(item, items, path=index) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 411, in descend for error in errors: File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/_validators.py", line 305, in properties yield from validator.descend( File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 411, in descend for error in errors: File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/_validators.py", line 284, in ref yield from validator._validate_reference(ref=ref, instance=instance) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 441, in _validate_reference resolved = self._resolver.lookup(ref) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/referencing/_core.py", line 586, in lookup retrieved = self._registry.get_or_retrieve(uri) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/referencing/_core.py", line 336, in get_or_retrieve resource = registry._retrieve(uri) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 120, in _warn_for_remote_retrieve return referencing.Resource.from_contents(json.load(response)) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/referencing/_core.py", line 129, in from_contents raise exceptions.CannotDetermineSpecification(contents) referencing.exceptions.CannotDetermineSpecification: {'enum': ['ENA', 'SRA', 'OAGR', 'UCPH ERDA', 'MG-RAST', 'GenBank', 'Dryad', 'Zenodo', 'GitHub']}

Ancient Single Genome Host Associated

Traceback (most recent call last): File "/opt/hostedtoolcache/Python/3.9.17/x64/bin/AMDirT", line 8, in sys.exit(cli()) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 1157, in call return self.main(args, kwargs) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 1078, in main rv = self.invoke(ctx) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 1688, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 1434, in invoke return ctx.invoke(self.callback, ctx.params) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 783, in invoke return __callback(args, *kwargs) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/decorators.py", line 33, in new_func return f(get_current_context(), args, kwargs) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/AMDirT/cli.py", line 78, in validate run_validation(kwargs, **ctx.obj) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/AMDirT/validate/init.py", line 21, in run_validation v.validate_schema() File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/AMDirT/validate/domain/init.py", line 235, in validate_schema for err in validator.iter_errors(self.dataset_json): File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 363, in iter_errors for error in errors: File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/_legacy_validators.py", line 115, in items_draft6_draft7_draft201909 yield from validator.descend(item, items, path=index) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 411, in descend for error in errors: File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/_validators.py", line 305, in properties yield from validator.descend( File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 411, in descend for error in errors: File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/_validators.py", line 284, in ref yield from validator._validate_reference(ref=ref, instance=instance) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 441, in _validate_reference resolved = self._resolver.lookup(ref) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/referencing/_core.py", line 586, in lookup retrieved = self._registry.get_or_retrieve(uri) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/referencing/_core.py", line 336, in get_or_retrieve resource = registry._retrieve(uri) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 120, in _warn_for_remote_retrieve return referencing.Resource.from_contents(json.load(response)) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/referencing/_core.py", line 129, in from_contents raise exceptions.CannotDetermineSpecification(contents) referencing.exceptions.CannotDetermineSpecification: {'enum': ['ENA', 'SRA', 'OAGR', 'UCPH ERDA', 'MG-RAST', 'GenBank', 'Dryad', 'Zenodo', 'GitHub']}

Ancient Metagenome Environmental

Traceback (most recent call last): File "/opt/hostedtoolcache/Python/3.9.17/x64/bin/AMDirT", line 8, in sys.exit(cli()) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 1157, in call return self.main(args, kwargs) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 1078, in main rv = self.invoke(ctx) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 1688, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 1434, in invoke return ctx.invoke(self.callback, ctx.params) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 783, in invoke return __callback(args, *kwargs) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/decorators.py", line 33, in new_func return f(get_current_context(), args, kwargs) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/AMDirT/cli.py", line 78, in validate run_validation(kwargs, **ctx.obj) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/AMDirT/validate/init.py", line 21, in run_validation v.validate_schema() File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/AMDirT/validate/domain/init.py", line 235, in validate_schema for err in validator.iter_errors(self.dataset_json): File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 363, in iter_errors for error in errors: File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/_legacy_validators.py", line 115, in items_draft6_draft7_draft201909 yield from validator.descend(item, items, path=index) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 411, in descend for error in errors: File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/_validators.py", line 305, in properties yield from validator.descend( File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 411, in descend for error in errors: File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/_validators.py", line 284, in ref yield from validator._validate_reference(ref=ref, instance=instance) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 441, in _validate_reference resolved = self._resolver.lookup(ref) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/referencing/_core.py", line 586, in lookup retrieved = self._registry.get_or_retrieve(uri) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/referencing/_core.py", line 336, in get_or_retrieve resource = registry._retrieve(uri) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 120, in _warn_for_remote_retrieve return referencing.Resource.from_contents(json.load(response)) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/referencing/_core.py", line 129, in from_contents raise exceptions.CannotDetermineSpecification(contents) referencing.exceptions.CannotDetermineSpecification: {'enum': ['ENA', 'SRA', 'OAGR', 'UCPH ERDA', 'MG-RAST', 'GenBank', 'Dryad', 'Zenodo', 'GitHub']}

github-actions[bot] commented 1 year ago

AMDirT, version 1.4.6

Samples

Ancient Metagenome Host Associated

Traceback (most recent call last): File "/opt/hostedtoolcache/Python/3.9.17/x64/bin/AMDirT", line 8, in sys.exit(cli()) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 1157, in call return self.main(args, kwargs) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 1078, in main rv = self.invoke(ctx) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 1688, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 1434, in invoke return ctx.invoke(self.callback, ctx.params) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 783, in invoke return __callback(args, *kwargs) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/decorators.py", line 33, in new_func return f(get_current_context(), args, kwargs) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/AMDirT/cli.py", line 78, in validate run_validation(kwargs, **ctx.obj) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/AMDirT/validate/init.py", line 21, in run_validation v.validate_schema() File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/AMDirT/validate/domain/init.py", line 235, in validate_schema for err in validator.iter_errors(self.dataset_json): File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 363, in iter_errors for error in errors: File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/_legacy_validators.py", line 115, in items_draft6_draft7_draft201909 yield from validator.descend(item, items, path=index) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 411, in descend for error in errors: File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/_validators.py", line 305, in properties yield from validator.descend( File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 411, in descend for error in errors: File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/_validators.py", line 284, in ref yield from validator._validate_reference(ref=ref, instance=instance) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 441, in _validate_reference resolved = self._resolver.lookup(ref) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/referencing/_core.py", line 586, in lookup retrieved = self._registry.get_or_retrieve(uri) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/referencing/_core.py", line 336, in get_or_retrieve resource = registry._retrieve(uri) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 120, in _warn_for_remote_retrieve return referencing.Resource.from_contents(json.load(response)) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/referencing/_core.py", line 129, in from_contents raise exceptions.CannotDetermineSpecification(contents) referencing.exceptions.CannotDetermineSpecification: {'enum': ['Afghanistan', 'Albania', 'Algeria', 'American Samoa', 'Andorra', 'Angola', 'Anguilla', 'Antarctica', 'Antigua and Barbuda', 'Arctic Ocean', 'Argentina', 'Armenia', 'Aruba', 'Ashmore and Cartier Islands', 'Atlantic Ocean', 'Australia', 'Austria', 'Azerbaijan', 'Bahamas', 'Bahrain', 'Baltic Sea', 'Baker Island', 'Bangladesh', 'Barbados', 'Bassas da India', 'Belarus', 'Belgium', 'Belize', 'Benin', 'Bermuda', 'Bhutan', 'Bolivia', 'Borneo', 'Bosnia and Herzegovina', 'Botswana', 'Bouvet Island', 'Brazil', 'British Virgin Islands', 'Brunei', 'Bulgaria', 'Burkina Faso', 'Burundi', 'Cambodia', 'Cameroon', 'Canada', 'Cape Verde', 'Cayman Islands', 'Central African Republic', 'Chad', 'Chile', 'China', 'Christmas Island', 'Clipperton Island', 'Cocos Islands', 'Colombia', 'Comoros', 'Cook Islands', 'Coral Sea Islands', 'Costa Rica', "Cote d'Ivoire", 'Croatia', 'Cuba', 'Curacao', 'Cyprus', 'Czech Republic', 'Democratic Republic of the Congo', 'Denmark', 'Djibouti', 'Dominica', 'Dominican Republic', 'Ecuador', 'Egypt', 'El Salvador', 'Equatorial Guinea', 'Eritrea', 'Estonia', 'Eswatini', 'Ethiopia', 'Europa Island', 'Falkland Islands (Islas Malvinas)', 'Faroe Islands', 'Fiji', 'Finland', 'France', 'French Guiana', 'French Polynesia', 'French Southern and Antarctic Lands', 'Gabon', 'Gambia', 'Gaza Strip', 'Georgia', 'Germany', 'Ghana', 'Gibraltar', 'Glorioso Islands', 'Greece', 'Greenland', 'Grenada', 'Guadeloupe', 'Guam', 'Guatemala', 'Guernsey', 'Guinea', 'Guinea-Bissau', 'Guyana', 'Haiti', 'Heard Island and McDonald Islands', 'Honduras', 'Hong Kong', 'Howland Island', 'Hungary', 'Iceland', 'India', 'Indian Ocean', 'Indonesia', 'Iran', 'Iraq', 'Ireland', 'Isle of Man', 'Israel', 'Italy', 'Jamaica', 'Jan Mayen', 'Japan', 'Jarvis Island', 'Jersey', 'Johnston Atoll', 'Jordan', 'Juan de Nova Island', 'Kazakhstan', 'Kenya', 'Kerguelen Archipelago', 'Kingman Reef', 'Kiribati', 'Kosovo', 'Kuwait', 'Kyrgyzstan', 'Laos', 'Latvia', 'Lebanon', 'Lesotho', 'Liberia', 'Libya', 'Liechtenstein', 'Line Islands', 'Lithuania', 'Luxembourg', 'Macau', 'Madagascar', 'Malawi', 'Malaysia', 'Maldives', 'Mali', 'Malta', 'Marshall Islands', 'Martinique', 'Mauritania', 'Mauritius', 'Mayotte', 'Mediterranean Sea', 'Mexico', 'Micronesia', 'Midway Islands', 'Moldova', 'Monaco', 'Mongolia', 'Montenegro', 'Montserrat', 'Morocco', 'Mozambique', 'Myanmar', 'Namibia', 'Nauru', 'Navassa Island', 'Nepal', 'Netherlands', 'New Caledonia', 'New Zealand', 'Nicaragua', 'Niger', 'Nigeria', 'Niue', 'Norfolk Island', 'North Korea', 'North Macedonia', 'North Sea', 'Northern Mariana Islands', 'Norway', 'Oman', 'Pacific Ocean', 'Pakistan', 'Palau', 'Palmyra Atoll', 'Panama', 'Papua New Guinea', 'Paracel Islands', 'Paraguay', 'Peru', 'Philippines', 'Pitcairn Islands', 'Poland', 'Portugal', 'Puerto Rico', 'Qatar', 'Republic of the Congo', 'Reunion', 'Romania', 'Ross Sea', 'Russia', 'Rwanda', 'Saint Helena', 'Saint Kitts and Nevis', 'Saint Lucia', 'Saint Pierre and Miquelon', 'Saint Vincent and the Grenadines', 'Samoa', 'San Marino', 'Sao Tome and Principe', 'Saudi Arabia', 'Senegal', 'Serbia', 'Seychelles', 'Sierra Leone', 'Singapore', 'Sint Maarten', 'Slovakia', 'Slovenia', 'Solomon Islands', 'Somalia', 'South Africa', 'South Georgia and the South Sandwich Islands', 'South Korea', 'South Sudan', 'Southern Ocean', 'Spain', 'Spratly Islands', 'Sri Lanka', 'State of Palestine', 'Sudan', 'Suriname', 'Svalbard', 'Sweden', 'Switzerland', 'Syria', 'Taiwan', 'Tajikistan', 'Tanzania', 'Tasman Sea', 'Thailand', 'Timor-Leste', 'Togo', 'Tokelau', 'Tonga', 'Trinidad and Tobago', 'Tromelin Island', 'Tunisia', 'Turkey', 'Turkmenistan', 'Turks and Caicos Islands', 'Tuvalu', 'USA', 'Uganda', 'Ukraine', 'United Arab Emirates', 'United Kingdom', 'Uruguay', 'Uzbekistan', 'Vanuatu', 'Venezuela', 'Viet Nam', 'Virgin Islands', 'Wake Island', 'Wallis and Futuna', 'West Bank', 'Western Sahara', 'Yemen', 'Zambia', 'Zimbabwe', 'Unknown']}

Ancient Single Genome Host Associated

Traceback (most recent call last): File "/opt/hostedtoolcache/Python/3.9.17/x64/bin/AMDirT", line 8, in sys.exit(cli()) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 1157, in call return self.main(args, kwargs) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 1078, in main rv = self.invoke(ctx) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 1688, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 1434, in invoke return ctx.invoke(self.callback, ctx.params) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 783, in invoke return __callback(args, *kwargs) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/decorators.py", line 33, in new_func return f(get_current_context(), args, kwargs) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/AMDirT/cli.py", line 78, in validate run_validation(kwargs, **ctx.obj) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/AMDirT/validate/init.py", line 21, in run_validation v.validate_schema() File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/AMDirT/validate/domain/init.py", line 235, in validate_schema for err in validator.iter_errors(self.dataset_json): File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 363, in iter_errors for error in errors: File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/_legacy_validators.py", line 115, in items_draft6_draft7_draft201909 yield from validator.descend(item, items, path=index) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 411, in descend for error in errors: File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/_validators.py", line 305, in properties yield from validator.descend( File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 411, in descend for error in errors: File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/_validators.py", line 284, in ref yield from validator._validate_reference(ref=ref, instance=instance) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 441, in _validate_reference resolved = self._resolver.lookup(ref) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/referencing/_core.py", line 586, in lookup retrieved = self._registry.get_or_retrieve(uri) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/referencing/_core.py", line 336, in get_or_retrieve resource = registry._retrieve(uri) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 120, in _warn_for_remote_retrieve return referencing.Resource.from_contents(json.load(response)) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/referencing/_core.py", line 129, in from_contents raise exceptions.CannotDetermineSpecification(contents) referencing.exceptions.CannotDetermineSpecification: {'enum': ['Afghanistan', 'Albania', 'Algeria', 'American Samoa', 'Andorra', 'Angola', 'Anguilla', 'Antarctica', 'Antigua and Barbuda', 'Arctic Ocean', 'Argentina', 'Armenia', 'Aruba', 'Ashmore and Cartier Islands', 'Atlantic Ocean', 'Australia', 'Austria', 'Azerbaijan', 'Bahamas', 'Bahrain', 'Baltic Sea', 'Baker Island', 'Bangladesh', 'Barbados', 'Bassas da India', 'Belarus', 'Belgium', 'Belize', 'Benin', 'Bermuda', 'Bhutan', 'Bolivia', 'Borneo', 'Bosnia and Herzegovina', 'Botswana', 'Bouvet Island', 'Brazil', 'British Virgin Islands', 'Brunei', 'Bulgaria', 'Burkina Faso', 'Burundi', 'Cambodia', 'Cameroon', 'Canada', 'Cape Verde', 'Cayman Islands', 'Central African Republic', 'Chad', 'Chile', 'China', 'Christmas Island', 'Clipperton Island', 'Cocos Islands', 'Colombia', 'Comoros', 'Cook Islands', 'Coral Sea Islands', 'Costa Rica', "Cote d'Ivoire", 'Croatia', 'Cuba', 'Curacao', 'Cyprus', 'Czech Republic', 'Democratic Republic of the Congo', 'Denmark', 'Djibouti', 'Dominica', 'Dominican Republic', 'Ecuador', 'Egypt', 'El Salvador', 'Equatorial Guinea', 'Eritrea', 'Estonia', 'Eswatini', 'Ethiopia', 'Europa Island', 'Falkland Islands (Islas Malvinas)', 'Faroe Islands', 'Fiji', 'Finland', 'France', 'French Guiana', 'French Polynesia', 'French Southern and Antarctic Lands', 'Gabon', 'Gambia', 'Gaza Strip', 'Georgia', 'Germany', 'Ghana', 'Gibraltar', 'Glorioso Islands', 'Greece', 'Greenland', 'Grenada', 'Guadeloupe', 'Guam', 'Guatemala', 'Guernsey', 'Guinea', 'Guinea-Bissau', 'Guyana', 'Haiti', 'Heard Island and McDonald Islands', 'Honduras', 'Hong Kong', 'Howland Island', 'Hungary', 'Iceland', 'India', 'Indian Ocean', 'Indonesia', 'Iran', 'Iraq', 'Ireland', 'Isle of Man', 'Israel', 'Italy', 'Jamaica', 'Jan Mayen', 'Japan', 'Jarvis Island', 'Jersey', 'Johnston Atoll', 'Jordan', 'Juan de Nova Island', 'Kazakhstan', 'Kenya', 'Kerguelen Archipelago', 'Kingman Reef', 'Kiribati', 'Kosovo', 'Kuwait', 'Kyrgyzstan', 'Laos', 'Latvia', 'Lebanon', 'Lesotho', 'Liberia', 'Libya', 'Liechtenstein', 'Line Islands', 'Lithuania', 'Luxembourg', 'Macau', 'Madagascar', 'Malawi', 'Malaysia', 'Maldives', 'Mali', 'Malta', 'Marshall Islands', 'Martinique', 'Mauritania', 'Mauritius', 'Mayotte', 'Mediterranean Sea', 'Mexico', 'Micronesia', 'Midway Islands', 'Moldova', 'Monaco', 'Mongolia', 'Montenegro', 'Montserrat', 'Morocco', 'Mozambique', 'Myanmar', 'Namibia', 'Nauru', 'Navassa Island', 'Nepal', 'Netherlands', 'New Caledonia', 'New Zealand', 'Nicaragua', 'Niger', 'Nigeria', 'Niue', 'Norfolk Island', 'North Korea', 'North Macedonia', 'North Sea', 'Northern Mariana Islands', 'Norway', 'Oman', 'Pacific Ocean', 'Pakistan', 'Palau', 'Palmyra Atoll', 'Panama', 'Papua New Guinea', 'Paracel Islands', 'Paraguay', 'Peru', 'Philippines', 'Pitcairn Islands', 'Poland', 'Portugal', 'Puerto Rico', 'Qatar', 'Republic of the Congo', 'Reunion', 'Romania', 'Ross Sea', 'Russia', 'Rwanda', 'Saint Helena', 'Saint Kitts and Nevis', 'Saint Lucia', 'Saint Pierre and Miquelon', 'Saint Vincent and the Grenadines', 'Samoa', 'San Marino', 'Sao Tome and Principe', 'Saudi Arabia', 'Senegal', 'Serbia', 'Seychelles', 'Sierra Leone', 'Singapore', 'Sint Maarten', 'Slovakia', 'Slovenia', 'Solomon Islands', 'Somalia', 'South Africa', 'South Georgia and the South Sandwich Islands', 'South Korea', 'South Sudan', 'Southern Ocean', 'Spain', 'Spratly Islands', 'Sri Lanka', 'State of Palestine', 'Sudan', 'Suriname', 'Svalbard', 'Sweden', 'Switzerland', 'Syria', 'Taiwan', 'Tajikistan', 'Tanzania', 'Tasman Sea', 'Thailand', 'Timor-Leste', 'Togo', 'Tokelau', 'Tonga', 'Trinidad and Tobago', 'Tromelin Island', 'Tunisia', 'Turkey', 'Turkmenistan', 'Turks and Caicos Islands', 'Tuvalu', 'USA', 'Uganda', 'Ukraine', 'United Arab Emirates', 'United Kingdom', 'Uruguay', 'Uzbekistan', 'Vanuatu', 'Venezuela', 'Viet Nam', 'Virgin Islands', 'Wake Island', 'Wallis and Futuna', 'West Bank', 'Western Sahara', 'Yemen', 'Zambia', 'Zimbabwe', 'Unknown']}

Ancient Metagenome Environmental

Traceback (most recent call last): File "/opt/hostedtoolcache/Python/3.9.17/x64/bin/AMDirT", line 8, in sys.exit(cli()) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 1157, in call return self.main(args, kwargs) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 1078, in main rv = self.invoke(ctx) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 1688, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 1434, in invoke return ctx.invoke(self.callback, ctx.params) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 783, in invoke return __callback(args, *kwargs) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/decorators.py", line 33, in new_func return f(get_current_context(), args, kwargs) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/AMDirT/cli.py", line 78, in validate run_validation(kwargs, **ctx.obj) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/AMDirT/validate/init.py", line 21, in run_validation v.validate_schema() File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/AMDirT/validate/domain/init.py", line 235, in validate_schema for err in validator.iter_errors(self.dataset_json): File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 363, in iter_errors for error in errors: File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/_legacy_validators.py", line 115, in items_draft6_draft7_draft201909 yield from validator.descend(item, items, path=index) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 411, in descend for error in errors: File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/_validators.py", line 305, in properties yield from validator.descend( File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 411, in descend for error in errors: File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/_validators.py", line 284, in ref yield from validator._validate_reference(ref=ref, instance=instance) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 441, in _validate_reference resolved = self._resolver.lookup(ref) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/referencing/_core.py", line 586, in lookup retrieved = self._registry.get_or_retrieve(uri) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/referencing/_core.py", line 336, in get_or_retrieve resource = registry._retrieve(uri) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 120, in _warn_for_remote_retrieve return referencing.Resource.from_contents(json.load(response)) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/referencing/_core.py", line 129, in from_contents raise exceptions.CannotDetermineSpecification(contents) referencing.exceptions.CannotDetermineSpecification: {'enum': ['Afghanistan', 'Albania', 'Algeria', 'American Samoa', 'Andorra', 'Angola', 'Anguilla', 'Antarctica', 'Antigua and Barbuda', 'Arctic Ocean', 'Argentina', 'Armenia', 'Aruba', 'Ashmore and Cartier Islands', 'Atlantic Ocean', 'Australia', 'Austria', 'Azerbaijan', 'Bahamas', 'Bahrain', 'Baltic Sea', 'Baker Island', 'Bangladesh', 'Barbados', 'Bassas da India', 'Belarus', 'Belgium', 'Belize', 'Benin', 'Bermuda', 'Bhutan', 'Bolivia', 'Borneo', 'Bosnia and Herzegovina', 'Botswana', 'Bouvet Island', 'Brazil', 'British Virgin Islands', 'Brunei', 'Bulgaria', 'Burkina Faso', 'Burundi', 'Cambodia', 'Cameroon', 'Canada', 'Cape Verde', 'Cayman Islands', 'Central African Republic', 'Chad', 'Chile', 'China', 'Christmas Island', 'Clipperton Island', 'Cocos Islands', 'Colombia', 'Comoros', 'Cook Islands', 'Coral Sea Islands', 'Costa Rica', "Cote d'Ivoire", 'Croatia', 'Cuba', 'Curacao', 'Cyprus', 'Czech Republic', 'Democratic Republic of the Congo', 'Denmark', 'Djibouti', 'Dominica', 'Dominican Republic', 'Ecuador', 'Egypt', 'El Salvador', 'Equatorial Guinea', 'Eritrea', 'Estonia', 'Eswatini', 'Ethiopia', 'Europa Island', 'Falkland Islands (Islas Malvinas)', 'Faroe Islands', 'Fiji', 'Finland', 'France', 'French Guiana', 'French Polynesia', 'French Southern and Antarctic Lands', 'Gabon', 'Gambia', 'Gaza Strip', 'Georgia', 'Germany', 'Ghana', 'Gibraltar', 'Glorioso Islands', 'Greece', 'Greenland', 'Grenada', 'Guadeloupe', 'Guam', 'Guatemala', 'Guernsey', 'Guinea', 'Guinea-Bissau', 'Guyana', 'Haiti', 'Heard Island and McDonald Islands', 'Honduras', 'Hong Kong', 'Howland Island', 'Hungary', 'Iceland', 'India', 'Indian Ocean', 'Indonesia', 'Iran', 'Iraq', 'Ireland', 'Isle of Man', 'Israel', 'Italy', 'Jamaica', 'Jan Mayen', 'Japan', 'Jarvis Island', 'Jersey', 'Johnston Atoll', 'Jordan', 'Juan de Nova Island', 'Kazakhstan', 'Kenya', 'Kerguelen Archipelago', 'Kingman Reef', 'Kiribati', 'Kosovo', 'Kuwait', 'Kyrgyzstan', 'Laos', 'Latvia', 'Lebanon', 'Lesotho', 'Liberia', 'Libya', 'Liechtenstein', 'Line Islands', 'Lithuania', 'Luxembourg', 'Macau', 'Madagascar', 'Malawi', 'Malaysia', 'Maldives', 'Mali', 'Malta', 'Marshall Islands', 'Martinique', 'Mauritania', 'Mauritius', 'Mayotte', 'Mediterranean Sea', 'Mexico', 'Micronesia', 'Midway Islands', 'Moldova', 'Monaco', 'Mongolia', 'Montenegro', 'Montserrat', 'Morocco', 'Mozambique', 'Myanmar', 'Namibia', 'Nauru', 'Navassa Island', 'Nepal', 'Netherlands', 'New Caledonia', 'New Zealand', 'Nicaragua', 'Niger', 'Nigeria', 'Niue', 'Norfolk Island', 'North Korea', 'North Macedonia', 'North Sea', 'Northern Mariana Islands', 'Norway', 'Oman', 'Pacific Ocean', 'Pakistan', 'Palau', 'Palmyra Atoll', 'Panama', 'Papua New Guinea', 'Paracel Islands', 'Paraguay', 'Peru', 'Philippines', 'Pitcairn Islands', 'Poland', 'Portugal', 'Puerto Rico', 'Qatar', 'Republic of the Congo', 'Reunion', 'Romania', 'Ross Sea', 'Russia', 'Rwanda', 'Saint Helena', 'Saint Kitts and Nevis', 'Saint Lucia', 'Saint Pierre and Miquelon', 'Saint Vincent and the Grenadines', 'Samoa', 'San Marino', 'Sao Tome and Principe', 'Saudi Arabia', 'Senegal', 'Serbia', 'Seychelles', 'Sierra Leone', 'Singapore', 'Sint Maarten', 'Slovakia', 'Slovenia', 'Solomon Islands', 'Somalia', 'South Africa', 'South Georgia and the South Sandwich Islands', 'South Korea', 'South Sudan', 'Southern Ocean', 'Spain', 'Spratly Islands', 'Sri Lanka', 'State of Palestine', 'Sudan', 'Suriname', 'Svalbard', 'Sweden', 'Switzerland', 'Syria', 'Taiwan', 'Tajikistan', 'Tanzania', 'Tasman Sea', 'Thailand', 'Timor-Leste', 'Togo', 'Tokelau', 'Tonga', 'Trinidad and Tobago', 'Tromelin Island', 'Tunisia', 'Turkey', 'Turkmenistan', 'Turks and Caicos Islands', 'Tuvalu', 'USA', 'Uganda', 'Ukraine', 'United Arab Emirates', 'United Kingdom', 'Uruguay', 'Uzbekistan', 'Vanuatu', 'Venezuela', 'Viet Nam', 'Virgin Islands', 'Wake Island', 'Wallis and Futuna', 'West Bank', 'Western Sahara', 'Yemen', 'Zambia', 'Zimbabwe', 'Unknown']}

Libraries

Ancient Metagenome Host Associated

Traceback (most recent call last): File "/opt/hostedtoolcache/Python/3.9.17/x64/bin/AMDirT", line 8, in sys.exit(cli()) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 1157, in call return self.main(args, kwargs) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 1078, in main rv = self.invoke(ctx) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 1688, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 1434, in invoke return ctx.invoke(self.callback, ctx.params) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 783, in invoke return __callback(args, *kwargs) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/decorators.py", line 33, in new_func return f(get_current_context(), args, kwargs) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/AMDirT/cli.py", line 78, in validate run_validation(kwargs, **ctx.obj) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/AMDirT/validate/init.py", line 21, in run_validation v.validate_schema() File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/AMDirT/validate/domain/init.py", line 235, in validate_schema for err in validator.iter_errors(self.dataset_json): File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 363, in iter_errors for error in errors: File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/_legacy_validators.py", line 115, in items_draft6_draft7_draft201909 yield from validator.descend(item, items, path=index) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 411, in descend for error in errors: File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/_validators.py", line 305, in properties yield from validator.descend( File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 411, in descend for error in errors: File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/_validators.py", line 284, in ref yield from validator._validate_reference(ref=ref, instance=instance) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 441, in _validate_reference resolved = self._resolver.lookup(ref) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/referencing/_core.py", line 586, in lookup retrieved = self._registry.get_or_retrieve(uri) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/referencing/_core.py", line 336, in get_or_retrieve resource = registry._retrieve(uri) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 120, in _warn_for_remote_retrieve return referencing.Resource.from_contents(json.load(response)) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/referencing/_core.py", line 129, in from_contents raise exceptions.CannotDetermineSpecification(contents) referencing.exceptions.CannotDetermineSpecification: {'enum': ['ENA', 'SRA', 'OAGR', 'UCPH ERDA', 'MG-RAST', 'GenBank', 'Dryad', 'Zenodo', 'GitHub']}

Ancient Single Genome Host Associated

Traceback (most recent call last): File "/opt/hostedtoolcache/Python/3.9.17/x64/bin/AMDirT", line 8, in sys.exit(cli()) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 1157, in call return self.main(args, kwargs) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 1078, in main rv = self.invoke(ctx) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 1688, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 1434, in invoke return ctx.invoke(self.callback, ctx.params) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 783, in invoke return __callback(args, *kwargs) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/decorators.py", line 33, in new_func return f(get_current_context(), args, kwargs) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/AMDirT/cli.py", line 78, in validate run_validation(kwargs, **ctx.obj) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/AMDirT/validate/init.py", line 21, in run_validation v.validate_schema() File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/AMDirT/validate/domain/init.py", line 235, in validate_schema for err in validator.iter_errors(self.dataset_json): File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 363, in iter_errors for error in errors: File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/_legacy_validators.py", line 115, in items_draft6_draft7_draft201909 yield from validator.descend(item, items, path=index) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 411, in descend for error in errors: File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/_validators.py", line 305, in properties yield from validator.descend( File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 411, in descend for error in errors: File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/_validators.py", line 284, in ref yield from validator._validate_reference(ref=ref, instance=instance) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 441, in _validate_reference resolved = self._resolver.lookup(ref) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/referencing/_core.py", line 586, in lookup retrieved = self._registry.get_or_retrieve(uri) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/referencing/_core.py", line 336, in get_or_retrieve resource = registry._retrieve(uri) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 120, in _warn_for_remote_retrieve return referencing.Resource.from_contents(json.load(response)) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/referencing/_core.py", line 129, in from_contents raise exceptions.CannotDetermineSpecification(contents) referencing.exceptions.CannotDetermineSpecification: {'enum': ['ENA', 'SRA', 'OAGR', 'UCPH ERDA', 'MG-RAST', 'GenBank', 'Dryad', 'Zenodo', 'GitHub']}

Ancient Metagenome Environmental

Traceback (most recent call last): File "/opt/hostedtoolcache/Python/3.9.17/x64/bin/AMDirT", line 8, in sys.exit(cli()) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 1157, in call return self.main(args, kwargs) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 1078, in main rv = self.invoke(ctx) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 1688, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 1434, in invoke return ctx.invoke(self.callback, ctx.params) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 783, in invoke return __callback(args, *kwargs) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/decorators.py", line 33, in new_func return f(get_current_context(), args, kwargs) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/AMDirT/cli.py", line 78, in validate run_validation(kwargs, **ctx.obj) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/AMDirT/validate/init.py", line 21, in run_validation v.validate_schema() File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/AMDirT/validate/domain/init.py", line 235, in validate_schema for err in validator.iter_errors(self.dataset_json): File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 363, in iter_errors for error in errors: File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/_legacy_validators.py", line 115, in items_draft6_draft7_draft201909 yield from validator.descend(item, items, path=index) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 411, in descend for error in errors: File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/_validators.py", line 305, in properties yield from validator.descend( File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 411, in descend for error in errors: File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/_validators.py", line 284, in ref yield from validator._validate_reference(ref=ref, instance=instance) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 441, in _validate_reference resolved = self._resolver.lookup(ref) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/referencing/_core.py", line 586, in lookup retrieved = self._registry.get_or_retrieve(uri) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/referencing/_core.py", line 336, in get_or_retrieve resource = registry._retrieve(uri) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/jsonschema/validators.py", line 120, in _warn_for_remote_retrieve return referencing.Resource.from_contents(json.load(response)) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/referencing/_core.py", line 129, in from_contents raise exceptions.CannotDetermineSpecification(contents) referencing.exceptions.CannotDetermineSpecification: {'enum': ['ENA', 'SRA', 'OAGR', 'UCPH ERDA', 'MG-RAST', 'GenBank', 'Dryad', 'Zenodo', 'GitHub']}

DianaSpurite commented 1 year ago

Getting the long error message just like with Neumann 2023 PR before

github-actions[bot] commented 1 year ago

AMDirT, version 1.4.6

Samples

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_samples.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_samples.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_samples.tsv is valid

Libraries

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_libraries.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_libraries.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_libraries.tsv is valid

github-actions[bot] commented 1 year ago

AMDirT, version 1.4.6

Samples

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_samples.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_samples.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_samples.tsv is valid

Libraries

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_libraries.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_libraries.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_libraries.tsv is valid

github-actions[bot] commented 1 year ago

AMDirT, version 1.4.6

Samples

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_samples.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_samples.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_samples.tsv is valid

Libraries

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_libraries.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_libraries.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_libraries.tsv is valid

SPAAM-community / AncientMetagenomeDir

Bonczarowska2023 #1097

Pull Request

New Publication

Publication Information

Checklist

Samples

Ancient Metagenome Host Associated

Ancient Single Genome Host Associated

Ancient Metagenome Environmental

Libraries

Ancient Metagenome Host Associated

Ancient Single Genome Host Associated

Ancient Metagenome Environmental

Samples

Ancient Metagenome Host Associated

Ancient Single Genome Host Associated

Ancient Metagenome Environmental

Libraries

Ancient Metagenome Host Associated

Ancient Single Genome Host Associated

Ancient Metagenome Environmental

Samples

Ancient Metagenome Host Associated

Ancient Single Genome Host Associated

Ancient Metagenome Environmental

Libraries

Ancient Metagenome Host Associated

Ancient Single Genome Host Associated

Ancient Metagenome Environmental

Samples

Ancient Metagenome Host Associated

Ancient Single Genome Host Associated

Ancient Metagenome Environmental

Libraries

Ancient Metagenome Host Associated

Ancient Single Genome Host Associated

Ancient Metagenome Environmental

Samples

Ancient Metagenome Host Associated

Ancient Single Genome Host Associated

Ancient Metagenome Environmental

Libraries

Ancient Metagenome Host Associated

Ancient Single Genome Host Associated

Ancient Metagenome Environmental