ktozdogan commented 1 year ago

Pull Request

This PR is for a

[x ] New Publication(s)
[ ] Correction

For the following list(s):

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

New Publication

Publication Information

This pull request is to add samples from the following publication(s): Armbrecht 2021, 10.1038/s43705-021-00070-8

This is to close #1046

Checklist

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

github-actions[bot] commented 1 year ago

AMDirT, version 1.4.6

Samples

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_samples.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_samples.tsv is valid

Ancient Metagenome Environmental

Traceback (most recent call last): File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/pandas/core/arrays/integer.py", line 51, in _safe_cast return values.astype(dtype, casting="safe", copy=copy) TypeError: Cannot cast array data from dtype('O') to dtype('int64') according to the rule 'safe'

The above exception was the direct cause of the following exception:

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 1130, in call return self.main(args, kwargs) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 1055, in main rv = self.invoke(ctx) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 1657, 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 1404, 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 760, in invoke return __callback(args, *kwargs) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/decorators.py", line 26, 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 19, in run_validation v = AMDirValidator(schema, dataset) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/AMDirT/validate/domain/init.py", line 89, in init self.dataset = self.read_dataset(dataset, self.schema) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/AMDirT/validate/domain/init.py", line 185, in read_dataset return pd.read_table(dataset, sep="\t", dtype=column_dtypes) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1242, in read_table return _read(filepath_or_buffer, kwds) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 583, in _read return parser.read(nrows) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1704, in read ) = self._engine.read( # type: ignore[attr-defined] File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 234, in read chunks = self._reader.read_low_memory(nrows) File "pandas/_libs/parsers.pyx", line 812, in pandas._libs.parsers.TextReader.read_low_memory File "pandas/_libs/parsers.pyx", line 889, in pandas._libs.parsers.TextReader._read_rows File "pandas/_libs/parsers.pyx", line 1034, in pandas._libs.parsers.TextReader._convert_column_data File "pandas/_libs/parsers.pyx", line 1073, in pandas._libs.parsers.TextReader._convert_tokens File "pandas/_libs/parsers.pyx", line 1177, in pandas._libs.parsers.TextReader._convert_with_dtype File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/pandas/core/arrays/numeric.py", line 289, in _from_sequence_of_strings return cls._from_sequence(scalars, dtype=dtype, copy=copy) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/pandas/core/arrays/masked.py", line 140, in _from_sequence values, mask = cls._coerce_to_array(scalars, dtype=dtype, copy=copy) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/pandas/core/arrays/numeric.py", line 277, in _coerce_toarray values, mask, , _ = _coerce_to_data_and_mask( File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/pandas/core/arrays/numeric.py", line 233, in _coerce_to_data_and_mask values = dtype_cls._safe_cast(values, dtype, copy=False) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/pandas/core/arrays/integer.py", line 57, in _safe_cast raise TypeError( TypeError: cannot safely cast non-equivalent object to int64

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

Invalid dataset ancientmetagenome-environmental_libraries.tsv

Error	Source	Column	Row	Message
Schema Validation Error	None	sample_name	638	None is not of type 'string'
Schema Validation Error	None	library_treatment	638	'None' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_treatment.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_treatment.json[/link]
Schema Validation Error	None	sample_name	639	None is not of type 'string'
Schema Validation Error	None	library_treatment	639	'None' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_treatment.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_treatment.json[/link]
Schema Validation Error	None	sample_name	640	None is not of type 'string'
Schema Validation Error	None	library_treatment	640	'None' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_treatment.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_treatment.json[/link]
Schema Validation Error	None	sample_name	641	None is not of type 'string'
Schema Validation Error	None	library_treatment	641	'None' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_treatment.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_treatment.json[/link]
Schema Validation Error	None	sample_name	642	None is not of type 'string'
Schema Validation Error	None	library_treatment	642	'None' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_treatment.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_treatment.json[/link]
Schema Validation Error	None	sample_name	643	None is not of type 'string'
Schema Validation Error	None	library_treatment	643	'None' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_treatment.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_treatment.json[/link]

github-actions[bot] commented 1 year ago

AMDirT, version 1.4.6

Samples

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_samples.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_samples.tsv is valid

Ancient Metagenome Environmental

Traceback (most recent call last): File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/pandas/core/arrays/integer.py", line 51, in _safe_cast return values.astype(dtype, casting="safe", copy=copy) TypeError: Cannot cast array data from dtype('O') to dtype('int64') according to the rule 'safe'

The above exception was the direct cause of the following exception:

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 1130, in call return self.main(args, kwargs) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 1055, in main rv = self.invoke(ctx) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 1657, 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 1404, 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 760, in invoke return __callback(args, *kwargs) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/decorators.py", line 26, 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 19, in run_validation v = AMDirValidator(schema, dataset) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/AMDirT/validate/domain/init.py", line 89, in init self.dataset = self.read_dataset(dataset, self.schema) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/AMDirT/validate/domain/init.py", line 185, in read_dataset return pd.read_table(dataset, sep="\t", dtype=column_dtypes) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1242, in read_table return _read(filepath_or_buffer, kwds) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 583, in _read return parser.read(nrows) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1704, in read ) = self._engine.read( # type: ignore[attr-defined] File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 234, in read chunks = self._reader.read_low_memory(nrows) File "pandas/_libs/parsers.pyx", line 812, in pandas._libs.parsers.TextReader.read_low_memory File "pandas/_libs/parsers.pyx", line 889, in pandas._libs.parsers.TextReader._read_rows File "pandas/_libs/parsers.pyx", line 1034, in pandas._libs.parsers.TextReader._convert_column_data File "pandas/_libs/parsers.pyx", line 1073, in pandas._libs.parsers.TextReader._convert_tokens File "pandas/_libs/parsers.pyx", line 1177, in pandas._libs.parsers.TextReader._convert_with_dtype File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/pandas/core/arrays/numeric.py", line 289, in _from_sequence_of_strings return cls._from_sequence(scalars, dtype=dtype, copy=copy) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/pandas/core/arrays/masked.py", line 140, in _from_sequence values, mask = cls._coerce_to_array(scalars, dtype=dtype, copy=copy) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/pandas/core/arrays/numeric.py", line 277, in _coerce_toarray values, mask, , _ = _coerce_to_data_and_mask( File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/pandas/core/arrays/numeric.py", line 233, in _coerce_to_data_and_mask values = dtype_cls._safe_cast(values, dtype, copy=False) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/pandas/core/arrays/integer.py", line 57, in _safe_cast raise TypeError( TypeError: cannot safely cast non-equivalent object to int64

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

Invalid dataset ancientmetagenome-environmental_libraries.tsv

Error	Source	Column	Row	Message
Schema Validation Error	34.288	archive	638	'34.288' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/archive.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/archive.json[/link]
Schema Validation Error	SBBasin	strand_type	638	'SBBasin' is not one of ['single', 'double', 'unknown']
Schema Validation Error	1.2	library_polymerase	638	'1.2' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	MV1012-002P	library_treatment	638	'MV1012-002P' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_treatment.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_treatment.json[/link]
Schema Validation Error	10.2973/odp.proc.sr.146-2.282.1995	instrument_model	638	'10.2973/odp.proc.sr.146-2.282.1995' 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	None	library_layout	638	None is not one of ['PAIRED', 'SINGLE']
Schema Validation Error	marine sediment	library_strategy	638	'marine sediment' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_strategy.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_strategy.json[/link]
Schema Validation Error	None	download_sizes	638	None is not of type 'string'
Schema Validation Error	34.288	archive	639	'34.288' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/archive.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/archive.json[/link]
Schema Validation Error	SBBasin	strand_type	639	'SBBasin' is not one of ['single', 'double', 'unknown']
Schema Validation Error	4.3	library_polymerase	639	'4.3' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	MV1012-002P	library_treatment	639	'MV1012-002P' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_treatment.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_treatment.json[/link]
Schema Validation Error	10.2973/odp.proc.sr.146-2.282.1995	instrument_model	639	'10.2973/odp.proc.sr.146-2.282.1995' 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	None	library_layout	639	None is not one of ['PAIRED', 'SINGLE']
Schema Validation Error	marine sediment	library_strategy	639	'marine sediment' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_strategy.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_strategy.json[/link]
Schema Validation Error	None	download_sizes	639	None is not of type 'string'
Schema Validation Error	34.288	archive	640	'34.288' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/archive.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/archive.json[/link]
Schema Validation Error	SBBasin	strand_type	640	'SBBasin' is not one of ['single', 'double', 'unknown']
Schema Validation Error	7.3	library_polymerase	640	'7.3' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	MV1012-002P	library_treatment	640	'MV1012-002P' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_treatment.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_treatment.json[/link]
Schema Validation Error	10.2973/odp.proc.sr.146-2.282.1995	instrument_model	640	'10.2973/odp.proc.sr.146-2.282.1995' 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	None	library_layout	640	None is not one of ['PAIRED', 'SINGLE']
Schema Validation Error	marine sediment	library_strategy	640	'marine sediment' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_strategy.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_strategy.json[/link]
Schema Validation Error	None	download_sizes	640	None is not of type 'string'
Schema Validation Error	34.288	archive	641	'34.288' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/archive.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/archive.json[/link]
Schema Validation Error	SBBasin	strand_type	641	'SBBasin' is not one of ['single', 'double', 'unknown']
Schema Validation Error	11.8	library_polymerase	641	'11.8' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	MV1012-002P	library_treatment	641	'MV1012-002P' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_treatment.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_treatment.json[/link]
Schema Validation Error	10.2973/odp.proc.sr.146-2.282.1995	instrument_model	641	'10.2973/odp.proc.sr.146-2.282.1995' 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	None	library_layout	641	None is not one of ['PAIRED', 'SINGLE']
Schema Validation Error	marine sediment	library_strategy	641	'marine sediment' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_strategy.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_strategy.json[/link]
Schema Validation Error	None	download_sizes	641	None is not of type 'string'
Schema Validation Error	34.288	archive	642	'34.288' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/archive.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/archive.json[/link]
Schema Validation Error	SBBasin	strand_type	642	'SBBasin' is not one of ['single', 'double', 'unknown']
Schema Validation Error	16.4	library_polymerase	642	'16.4' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	MV1012-002P	library_treatment	642	'MV1012-002P' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_treatment.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_treatment.json[/link]
Schema Validation Error	10.2973/odp.proc.sr.146-2.282.1995	instrument_model	642	'10.2973/odp.proc.sr.146-2.282.1995' 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	None	library_layout	642	None is not one of ['PAIRED', 'SINGLE']
Schema Validation Error	marine sediment	library_strategy	642	'marine sediment' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_strategy.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_strategy.json[/link]
Schema Validation Error	None	download_sizes	642	None is not of type 'string'

github-actions[bot] commented 1 year ago

AMDirT, version 1.4.6

Samples

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_samples.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_samples.tsv is valid

Ancient Metagenome Environmental

Traceback (most recent call last): File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/pandas/core/arrays/integer.py", line 51, in _safe_cast return values.astype(dtype, casting="safe", copy=copy) TypeError: Cannot cast array data from dtype('O') to dtype('int64') according to the rule 'safe'

The above exception was the direct cause of the following exception:

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 1130, in call return self.main(args, kwargs) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 1055, in main rv = self.invoke(ctx) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 1657, 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 1404, 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 760, in invoke return __callback(args, *kwargs) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/decorators.py", line 26, 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 19, in run_validation v = AMDirValidator(schema, dataset) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/AMDirT/validate/domain/init.py", line 89, in init self.dataset = self.read_dataset(dataset, self.schema) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/AMDirT/validate/domain/init.py", line 185, in read_dataset return pd.read_table(dataset, sep="\t", dtype=column_dtypes) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1242, in read_table return _read(filepath_or_buffer, kwds) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 583, in _read return parser.read(nrows) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1704, in read ) = self._engine.read( # type: ignore[attr-defined] File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 234, in read chunks = self._reader.read_low_memory(nrows) File "pandas/_libs/parsers.pyx", line 812, in pandas._libs.parsers.TextReader.read_low_memory File "pandas/_libs/parsers.pyx", line 889, in pandas._libs.parsers.TextReader._read_rows File "pandas/_libs/parsers.pyx", line 1034, in pandas._libs.parsers.TextReader._convert_column_data File "pandas/_libs/parsers.pyx", line 1073, in pandas._libs.parsers.TextReader._convert_tokens File "pandas/_libs/parsers.pyx", line 1177, in pandas._libs.parsers.TextReader._convert_with_dtype File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/pandas/core/arrays/numeric.py", line 289, in _from_sequence_of_strings return cls._from_sequence(scalars, dtype=dtype, copy=copy) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/pandas/core/arrays/masked.py", line 140, in _from_sequence values, mask = cls._coerce_to_array(scalars, dtype=dtype, copy=copy) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/pandas/core/arrays/numeric.py", line 277, in _coerce_toarray values, mask, , _ = _coerce_to_data_and_mask( File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/pandas/core/arrays/numeric.py", line 233, in _coerce_to_data_and_mask values = dtype_cls._safe_cast(values, dtype, copy=False) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/pandas/core/arrays/integer.py", line 57, in _safe_cast raise TypeError( TypeError: cannot safely cast non-equivalent object to int64

Libraries

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_libraries.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_libraries.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_libraries.tsv is valid

github-actions[bot] commented 1 year ago

AMDirT, version 1.4.6

Samples

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_samples.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_samples.tsv is valid

Ancient Metagenome Environmental

Traceback (most recent call last): File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/pandas/core/arrays/integer.py", line 51, in _safe_cast return values.astype(dtype, casting="safe", copy=copy) TypeError: Cannot cast array data from dtype('O') to dtype('int64') according to the rule 'safe'

The above exception was the direct cause of the following exception:

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 1130, in call return self.main(args, kwargs) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 1055, in main rv = self.invoke(ctx) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 1657, 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 1404, 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 760, in invoke return __callback(args, *kwargs) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/decorators.py", line 26, 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 19, in run_validation v = AMDirValidator(schema, dataset) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/AMDirT/validate/domain/init.py", line 89, in init self.dataset = self.read_dataset(dataset, self.schema) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/AMDirT/validate/domain/init.py", line 185, in read_dataset return pd.read_table(dataset, sep="\t", dtype=column_dtypes) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1242, in read_table return _read(filepath_or_buffer, kwds) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 583, in _read return parser.read(nrows) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1704, in read ) = self._engine.read( # type: ignore[attr-defined] File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 234, in read chunks = self._reader.read_low_memory(nrows) File "pandas/_libs/parsers.pyx", line 812, in pandas._libs.parsers.TextReader.read_low_memory File "pandas/_libs/parsers.pyx", line 889, in pandas._libs.parsers.TextReader._read_rows File "pandas/_libs/parsers.pyx", line 1034, in pandas._libs.parsers.TextReader._convert_column_data File "pandas/_libs/parsers.pyx", line 1073, in pandas._libs.parsers.TextReader._convert_tokens File "pandas/_libs/parsers.pyx", line 1177, in pandas._libs.parsers.TextReader._convert_with_dtype File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/pandas/core/arrays/numeric.py", line 289, in _from_sequence_of_strings return cls._from_sequence(scalars, dtype=dtype, copy=copy) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/pandas/core/arrays/masked.py", line 140, in _from_sequence values, mask = cls._coerce_to_array(scalars, dtype=dtype, copy=copy) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/pandas/core/arrays/numeric.py", line 277, in _coerce_toarray values, mask, , _ = _coerce_to_data_and_mask( File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/pandas/core/arrays/numeric.py", line 233, in _coerce_to_data_and_mask values = dtype_cls._safe_cast(values, dtype, copy=False) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/pandas/core/arrays/integer.py", line 57, in _safe_cast raise TypeError( TypeError: cannot safely cast non-equivalent object to int64

Libraries

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_libraries.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_libraries.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_libraries.tsv is valid

github-actions[bot] commented 1 year ago

AMDirT, version 1.4.6

Samples

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_samples.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_samples.tsv is valid

Ancient Metagenome Environmental

Traceback (most recent call last): File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/pandas/core/arrays/integer.py", line 51, in _safe_cast return values.astype(dtype, casting="safe", copy=copy) TypeError: Cannot cast array data from dtype('O') to dtype('int64') according to the rule 'safe'

The above exception was the direct cause of the following exception:

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 1130, in call return self.main(args, kwargs) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 1055, in main rv = self.invoke(ctx) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/core.py", line 1657, 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 1404, 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 760, in invoke return __callback(args, *kwargs) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/click/decorators.py", line 26, 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 19, in run_validation v = AMDirValidator(schema, dataset) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/AMDirT/validate/domain/init.py", line 89, in init self.dataset = self.read_dataset(dataset, self.schema) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/AMDirT/validate/domain/init.py", line 185, in read_dataset return pd.read_table(dataset, sep="\t", dtype=column_dtypes) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1242, in read_table return _read(filepath_or_buffer, kwds) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 583, in _read return parser.read(nrows) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1704, in read ) = self._engine.read( # type: ignore[attr-defined] File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 234, in read chunks = self._reader.read_low_memory(nrows) File "pandas/_libs/parsers.pyx", line 812, in pandas._libs.parsers.TextReader.read_low_memory File "pandas/_libs/parsers.pyx", line 889, in pandas._libs.parsers.TextReader._read_rows File "pandas/_libs/parsers.pyx", line 1034, in pandas._libs.parsers.TextReader._convert_column_data File "pandas/_libs/parsers.pyx", line 1073, in pandas._libs.parsers.TextReader._convert_tokens File "pandas/_libs/parsers.pyx", line 1177, in pandas._libs.parsers.TextReader._convert_with_dtype File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/pandas/core/arrays/numeric.py", line 289, in _from_sequence_of_strings return cls._from_sequence(scalars, dtype=dtype, copy=copy) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/pandas/core/arrays/masked.py", line 140, in _from_sequence values, mask = cls._coerce_to_array(scalars, dtype=dtype, copy=copy) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/pandas/core/arrays/numeric.py", line 277, in _coerce_toarray values, mask, , _ = _coerce_to_data_and_mask( File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/pandas/core/arrays/numeric.py", line 233, in _coerce_to_data_and_mask values = dtype_cls._safe_cast(values, dtype, copy=False) File "/opt/hostedtoolcache/Python/3.9.17/x64/lib/python3.9/site-packages/pandas/core/arrays/integer.py", line 57, in _safe_cast raise TypeError( TypeError: cannot safely cast non-equivalent object to int64

Libraries

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_libraries.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_libraries.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_libraries.tsv is valid

github-actions[bot] commented 1 year ago

AMDirT, version 1.4.6

Samples

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_samples.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_samples.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_samples.tsv is valid

Libraries

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_libraries.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_libraries.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_libraries.tsv is valid

github-actions[bot] commented 1 year ago

AMDirT, version 1.4.6

Samples

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_samples.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_samples.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_samples.tsv is valid

Libraries

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_libraries.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_libraries.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_libraries.tsv is valid

github-actions[bot] commented 1 year ago

AMDirT, version 1.4.6

Samples

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_samples.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_samples.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_samples.tsv is valid

Libraries

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_libraries.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_libraries.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_libraries.tsv is valid

SPAAM-community / AncientMetagenomeDir

Armbrecht2021 #1087

Pull Request

New Publication

Publication Information

Checklist

Samples

Ancient Metagenome Host Associated

Ancient Single Genome Host Associated

Ancient Metagenome Environmental

Libraries

Ancient Metagenome Host Associated

Ancient Single Genome Host Associated

Ancient Metagenome Environmental

Samples

Ancient Metagenome Host Associated

Ancient Single Genome Host Associated

Ancient Metagenome Environmental

Libraries

Ancient Metagenome Host Associated

Ancient Single Genome Host Associated

Ancient Metagenome Environmental

Samples

Ancient Metagenome Host Associated

Ancient Single Genome Host Associated

Ancient Metagenome Environmental

Libraries

Ancient Metagenome Host Associated

Ancient Single Genome Host Associated

Ancient Metagenome Environmental

Samples

Ancient Metagenome Host Associated

Ancient Single Genome Host Associated

Ancient Metagenome Environmental

Libraries

Ancient Metagenome Host Associated

Ancient Single Genome Host Associated

Ancient Metagenome Environmental

Samples

Ancient Metagenome Host Associated

Ancient Single Genome Host Associated

Ancient Metagenome Environmental

Libraries

Ancient Metagenome Host Associated

Ancient Single Genome Host Associated

Ancient Metagenome Environmental

Samples

Ancient Metagenome Host Associated

Ancient Single Genome Host Associated

Ancient Metagenome Environmental

Libraries

Ancient Metagenome Host Associated

Ancient Single Genome Host Associated

Ancient Metagenome Environmental

Samples

Ancient Metagenome Host Associated

Ancient Single Genome Host Associated

Ancient Metagenome Environmental

Libraries

Ancient Metagenome Host Associated

Ancient Single Genome Host Associated

Ancient Metagenome Environmental

Samples

Ancient Metagenome Host Associated

Ancient Single Genome Host Associated

Ancient Metagenome Environmental

Libraries

Ancient Metagenome Host Associated

Ancient Single Genome Host Associated

Ancient Metagenome Environmental