Neumann2023

[DianaSpurite]

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://austriaca.at/bronzezeit-pest-in-drasenhofen

This is to close #1092

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'?
• [x] Pull request has passed validation checks (see automated comment from github-bot)?
• [x] 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]]

AMDirT, version 1.4.6

Samples

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_samples.tsv is valid

Ancient Single Genome Host Associated

Invalid dataset ancientsinglegenome-hostassociated_samples.tsv

Error	Source	Column	Row	Message
Schema Validation Error	Neumann 2023	project_name	588	'Neumann 2023' does not match '^[a-zA-Z]+\d{4}[b-z]?$'
Schema Validation Error	austriaca.at/bronzezeit-pest-in-drasenhofen	publication_doi	588	'austriaca.at/bronzezeit-pest-in-drasenhofen' does not match '^10.\d{4,9}\/[^,]+$'
Schema Validation Error	austriaca.at/bronzezeit-pest-in-drasenhofen	sample_age_doi	588	'austriaca.at/bronzezeit-pest-in-drasenhofen' does not match '^10.\d{4,9}\/[^,]+$'
Schema Validation Error	Neumann 2023	project_name	589	'Neumann 2023' does not match '^[a-zA-Z]+\d{4}[b-z]?$'
Schema Validation Error	austriaca.at/bronzezeit-pest-in-drasenhofen	publication_doi	589	'austriaca.at/bronzezeit-pest-in-drasenhofen' does not match '^10.\d{4,9}\/[^,]+$'
Schema Validation Error	austriaca.at/bronzezeit-pest-in-drasenhofen	sample_age_doi	589	'austriaca.at/bronzezeit-pest-in-drasenhofen' does not match '^10.\d{4,9}\/[^,]+$'

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

Invalid dataset ancientsinglegenome-hostassociated_libraries.tsv

Error	Source	Column	Row	Message
Schema Validation Error	Neumann 2023	project_name	2304	'Neumann 2023' does not match '^[a-zA-Z]+\d{4}[b-z]?$'
Schema Validation Error	austriaca.at/bronzezeit-pest-in-drasenhofen	data_publication_doi	2304	'austriaca.at/bronzezeit-pest-in-drasenhofen' does not match '^10.\d{4,9}\/[^,]+$'
Schema Validation Error	Neumann 2023	project_name	2305	'Neumann 2023' does not match '^[a-zA-Z]+\d{4}[b-z]?$'
Schema Validation Error	austriaca.at/bronzezeit-pest-in-drasenhofen	data_publication_doi	2305	'austriaca.at/bronzezeit-pest-in-drasenhofen' does not match '^10.\d{4,9}\/[^,]+$'
Schema Validation Error	Neumann 2023	project_name	2306	'Neumann 2023' does not match '^[a-zA-Z]+\d{4}[b-z]?$'
Schema Validation Error	austriaca.at/bronzezeit-pest-in-drasenhofen	data_publication_doi	2306	'austriaca.at/bronzezeit-pest-in-drasenhofen' does not match '^10.\d{4,9}\/[^,]+$'
Schema Validation Error	Neumann 2023	project_name	2307	'Neumann 2023' does not match '^[a-zA-Z]+\d{4}[b-z]?$'
Schema Validation Error	austriaca.at/bronzezeit-pest-in-drasenhofen	data_publication_doi	2307	'austriaca.at/bronzezeit-pest-in-drasenhofen' does not match '^10.\d{4,9}\/[^,]+$'

Ancient Metagenome Environmental

ancientmetagenome-environmental_libraries.tsv is valid

[github-actions[bot]]

AMDirT, version 1.4.6

Samples

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_samples.tsv is valid

Ancient Single Genome Host Associated

Invalid dataset ancientsinglegenome-hostassociated_samples.tsv

Error	Source	Column	Row	Message
Schema Validation Error	Neumann 2023	project_name	588	'Neumann 2023' does not match '^[a-zA-Z]+\d{4}[b-z]?$'
Schema Validation Error	austriaca.at/bronzezeit-pest-in-drasenhofen	publication_doi	588	'austriaca.at/bronzezeit-pest-in-drasenhofen' does not match '^10.\d{4,9}\/[^,]+$'
Schema Validation Error	austriaca.at/bronzezeit-pest-in-drasenhofen	sample_age_doi	588	'austriaca.at/bronzezeit-pest-in-drasenhofen' does not match '^10.\d{4,9}\/[^,]+$'
Schema Validation Error	Neumann 2023	project_name	589	'Neumann 2023' does not match '^[a-zA-Z]+\d{4}[b-z]?$'
Schema Validation Error	austriaca.at/bronzezeit-pest-in-drasenhofen	publication_doi	589	'austriaca.at/bronzezeit-pest-in-drasenhofen' does not match '^10.\d{4,9}\/[^,]+$'
Schema Validation Error	austriaca.at/bronzezeit-pest-in-drasenhofen	sample_age_doi	589	'austriaca.at/bronzezeit-pest-in-drasenhofen' does not match '^10.\d{4,9}\/[^,]+$'

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

Invalid dataset ancientsinglegenome-hostassociated_libraries.tsv

Error	Source	Column	Row	Message
Schema Validation Error	Neumann 2023	project_name	2304	'Neumann 2023' does not match '^[a-zA-Z]+\d{4}[b-z]?$'
Schema Validation Error	austriaca.at/bronzezeit-pest-in-drasenhofen	data_publication_doi	2304	'austriaca.at/bronzezeit-pest-in-drasenhofen' does not match '^10.\d{4,9}\/[^,]+$'
Schema Validation Error	Neumann 2023	project_name	2305	'Neumann 2023' does not match '^[a-zA-Z]+\d{4}[b-z]?$'
Schema Validation Error	austriaca.at/bronzezeit-pest-in-drasenhofen	data_publication_doi	2305	'austriaca.at/bronzezeit-pest-in-drasenhofen' does not match '^10.\d{4,9}\/[^,]+$'
Schema Validation Error	Neumann 2023	project_name	2306	'Neumann 2023' does not match '^[a-zA-Z]+\d{4}[b-z]?$'
Schema Validation Error	austriaca.at/bronzezeit-pest-in-drasenhofen	data_publication_doi	2306	'austriaca.at/bronzezeit-pest-in-drasenhofen' does not match '^10.\d{4,9}\/[^,]+$'
Schema Validation Error	Neumann 2023	project_name	2307	'Neumann 2023' does not match '^[a-zA-Z]+\d{4}[b-z]?$'
Schema Validation Error	austriaca.at/bronzezeit-pest-in-drasenhofen	data_publication_doi	2307	'austriaca.at/bronzezeit-pest-in-drasenhofen' does not match '^10.\d{4,9}\/[^,]+$'

Ancient Metagenome Environmental

ancientmetagenome-environmental_libraries.tsv is valid

[github-actions[bot]]

AMDirT, version 1.4.6

Samples

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_samples.tsv is valid

Ancient Single Genome Host Associated

Invalid dataset ancientsinglegenome-hostassociated_samples.tsv

Error	Source	Column	Row	Message
Schema Validation Error	austriaca.at/bronzezeit-pest-in-drasenhofen	publication_doi	588	'austriaca.at/bronzezeit-pest-in-drasenhofen' does not match '^10.\d{4,9}\/[^,]+$'
Schema Validation Error	austriaca.at/bronzezeit-pest-in-drasenhofen	sample_age_doi	588	'austriaca.at/bronzezeit-pest-in-drasenhofen' does not match '^10.\d{4,9}\/[^,]+$'
Schema Validation Error	austriaca.at/bronzezeit-pest-in-drasenhofen	publication_doi	589	'austriaca.at/bronzezeit-pest-in-drasenhofen' does not match '^10.\d{4,9}\/[^,]+$'
Schema Validation Error	austriaca.at/bronzezeit-pest-in-drasenhofen	sample_age_doi	589	'austriaca.at/bronzezeit-pest-in-drasenhofen' does not match '^10.\d{4,9}\/[^,]+$'

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

Invalid dataset ancientsinglegenome-hostassociated_libraries.tsv

Error	Source	Column	Row	Message
Schema Validation Error	Neumann 2023	project_name	2304	'Neumann 2023' does not match '^[a-zA-Z]+\d{4}[b-z]?$'
Schema Validation Error	austriaca.at/bronzezeit-pest-in-drasenhofen	data_publication_doi	2304	'austriaca.at/bronzezeit-pest-in-drasenhofen' does not match '^10.\d{4,9}\/[^,]+$'
Schema Validation Error	Neumann 2023	project_name	2305	'Neumann 2023' does not match '^[a-zA-Z]+\d{4}[b-z]?$'
Schema Validation Error	austriaca.at/bronzezeit-pest-in-drasenhofen	data_publication_doi	2305	'austriaca.at/bronzezeit-pest-in-drasenhofen' does not match '^10.\d{4,9}\/[^,]+$'
Schema Validation Error	Neumann 2023	project_name	2306	'Neumann 2023' does not match '^[a-zA-Z]+\d{4}[b-z]?$'
Schema Validation Error	austriaca.at/bronzezeit-pest-in-drasenhofen	data_publication_doi	2306	'austriaca.at/bronzezeit-pest-in-drasenhofen' does not match '^10.\d{4,9}\/[^,]+$'
Schema Validation Error	Neumann 2023	project_name	2307	'Neumann 2023' does not match '^[a-zA-Z]+\d{4}[b-z]?$'
Schema Validation Error	austriaca.at/bronzezeit-pest-in-drasenhofen	data_publication_doi	2307	'austriaca.at/bronzezeit-pest-in-drasenhofen' does not match '^10.\d{4,9}\/[^,]+$'

Ancient Metagenome Environmental

ancientmetagenome-environmental_libraries.tsv is valid

[github-actions[bot]]

AMDirT, version 1.4.6

Samples

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_samples.tsv is valid

Ancient Single Genome Host Associated

Invalid dataset ancientsinglegenome-hostassociated_samples.tsv

Error	Source	Column	Row	Message
Schema Validation Error	austriaca.at/bronzezeit-pest-in-drasenhofen	publication_doi	588	'austriaca.at/bronzezeit-pest-in-drasenhofen' does not match '^10.\d{4,9}\/[^,]+$'
Schema Validation Error	austriaca.at/bronzezeit-pest-in-drasenhofen	sample_age_doi	588	'austriaca.at/bronzezeit-pest-in-drasenhofen' does not match '^10.\d{4,9}\/[^,]+$'
Schema Validation Error	austriaca.at/bronzezeit-pest-in-drasenhofen	publication_doi	589	'austriaca.at/bronzezeit-pest-in-drasenhofen' does not match '^10.\d{4,9}\/[^,]+$'
Schema Validation Error	austriaca.at/bronzezeit-pest-in-drasenhofen	sample_age_doi	589	'austriaca.at/bronzezeit-pest-in-drasenhofen' does not match '^10.\d{4,9}\/[^,]+$'

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

Invalid dataset ancientsinglegenome-hostassociated_libraries.tsv

Error	Source	Column	Row	Message
Schema Validation Error	austriaca.at/bronzezeit-pest-in-drasenhofen	data_publication_doi	2304	'austriaca.at/bronzezeit-pest-in-drasenhofen' does not match '^10.\d{4,9}\/[^,]+$'
Schema Validation Error	austriaca.at/bronzezeit-pest-in-drasenhofen	data_publication_doi	2305	'austriaca.at/bronzezeit-pest-in-drasenhofen' does not match '^10.\d{4,9}\/[^,]+$'
Schema Validation Error	austriaca.at/bronzezeit-pest-in-drasenhofen	data_publication_doi	2306	'austriaca.at/bronzezeit-pest-in-drasenhofen' does not match '^10.\d{4,9}\/[^,]+$'
Schema Validation Error	austriaca.at/bronzezeit-pest-in-drasenhofen	data_publication_doi	2307	'austriaca.at/bronzezeit-pest-in-drasenhofen' does not match '^10.\d{4,9}\/[^,]+$'

Ancient Metagenome Environmental

ancientmetagenome-environmental_libraries.tsv is valid

[DianaSpurite]

1. library_polymerase as always in a different dimension
2. also didn't find a doi

[github-actions[bot]]

AMDirT, version 1.4.6

Samples

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_samples.tsv is valid

Ancient Single Genome Host Associated

Invalid dataset ancientsinglegenome-hostassociated_samples.tsv

Error	Source	Column	Row	Message
Schema Validation Error	austriaca.at/bronzezeit-pest-in-drasenhofen	publication_doi	588	'austriaca.at/bronzezeit-pest-in-drasenhofen' does not match '^10.\d{4,9}\/[^,]+$'
Schema Validation Error	austriaca.at/bronzezeit-pest-in-drasenhofen	sample_age_doi	588	'austriaca.at/bronzezeit-pest-in-drasenhofen' does not match '^10.\d{4,9}\/[^,]+$'
Schema Validation Error	austriaca.at/bronzezeit-pest-in-drasenhofen	publication_doi	589	'austriaca.at/bronzezeit-pest-in-drasenhofen' does not match '^10.\d{4,9}\/[^,]+$'
Schema Validation Error	austriaca.at/bronzezeit-pest-in-drasenhofen	sample_age_doi	589	'austriaca.at/bronzezeit-pest-in-drasenhofen' does not match '^10.\d{4,9}\/[^,]+$'

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]]

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]]

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 34, 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 354, 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 402, 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 402, 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 432, 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 34, 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 354, 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 402, 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 402, 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 432, 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 34, 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 354, 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 402, 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 402, 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 432, 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 34, 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 354, 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 402, 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 402, 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 432, 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 34, 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 354, 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 402, 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 402, 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 432, 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 34, 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 354, 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 402, 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 402, 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 432, 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]]

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 34, 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 354, 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 402, 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 402, 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 432, 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 34, 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 354, 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 402, 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 402, 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 432, 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 34, 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 354, 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 402, 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 402, 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 432, 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 34, 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 354, 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 402, 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 402, 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 432, 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 34, 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 354, 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 402, 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 402, 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 432, 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 34, 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 354, 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 402, 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 402, 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 432, 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]]

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 34, 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 354, 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 402, 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 402, 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 432, 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 34, 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 354, 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 402, 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 402, 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 432, 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 34, 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 354, 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 402, 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 402, 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 432, 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 34, 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 354, 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 402, 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 402, 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 432, 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 34, 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 354, 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 402, 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 402, 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 432, 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 34, 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 354, 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 402, 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 402, 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 432, 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]]

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 34, 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 354, 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 402, 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 402, 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 432, 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 34, 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 354, 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 402, 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 402, 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 432, 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 34, 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 354, 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 402, 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 402, 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 432, 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 34, 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 354, 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 402, 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 402, 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 432, 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 34, 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 354, 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 402, 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 402, 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 432, 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 34, 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 354, 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 402, 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 402, 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 432, 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]]

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 34, 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 354, 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 402, 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 402, 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 432, 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 34, 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 354, 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 402, 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 402, 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 432, 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 34, 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 354, 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 402, 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 402, 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 432, 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 34, 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 354, 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 402, 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 402, 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 432, 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 34, 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 354, 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 402, 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 402, 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 432, 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 34, 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 354, 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 402, 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 402, 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 432, 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]]

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

[jfy133]

Bug was due to https://github.com/SPAAM-community/AMDirT/issues/125, I've pinned the JSONschema package for you and will keep that temporarily now

[github-actions[bot]]

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]]

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

Invalid dataset ancientsinglegenome-hostassociated_libraries.tsv

Error	Source	Column	Row	Message
Schema Validation Error	Neumann 2023	project_name	2308	'Neumann 2023' does not match '^[a-zA-Z]+\d{4}[b-z]?$'
Schema Validation Error	Illumina HiSeq 4000 sequencing	instrument_model	2308	'Illumina HiSeq 4000 sequencing' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/instrument_model.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/instrument_model.json[/link]
Schema Validation Error	Neumann 2023	project_name	2309	'Neumann 2023' does not match '^[a-zA-Z]+\d{4}[b-z]?$'
Schema Validation Error	Illumina HiSeq 4000 sequencing	instrument_model	2309	'Illumina HiSeq 4000 sequencing' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/instrument_model.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/instrument_model.json[/link]

Ancient Metagenome Environmental

ancientmetagenome-environmental_libraries.tsv is valid

[DianaSpurite]

Single stranded for the shotgun sequence liraries (2 missing from library list!), and this was with no UDG treatmenment

Added the two libraries

Also the Gansauge is also cited for the capture libraries so they should also be singlestranded not doublre

changed

Polymerase for Gansauge 2020 is: AccuPrime Pfx DNA

added

[github-actions[bot]]

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]]

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]]

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

[jfy133]

I approve on behalf of @GUNeumann as his requested changes overlapped with mine and/or has been addressed as requested