mztab_logical_error.properties

l_code_NULL=2000
l_original_NULL=Column "{0}" is an empty cell, or the current column cannot use "null".
l_cause_NULL=In the table-based sections there MUST NOT be any empty cells. Missing values MUST be reported using "null".


l_code_NotNULL=2001
l_original_NotNULL=Column "{0}" field value does not allow a "null" value.
l_cause_NotNULL=Some field values disallow a "null" or empty value. In general, "null" values SHOULD not be given within any column of a "Complete" file, only to indicate that values were truly absent.


l_code_LineOrder=2002
l_original_LineOrder=Current line belongs to "{0}" section, "{1}" line can not be displayed here.
l_cause_LineOrder=mzTab line including main sections: metadata, small molecule summary, small molecule feature, small molecule evidence. Every section in an mzTab file MUST only occur once (if present). The line order MUST be the following one: metadata lines should be displayed first, then the small molecule header, followed by small molecule summary lines, followed by small molecule feature header, then small molecule feature lines, followed by small molecule evidence, followed by small molecule evidence lines.


l_code_HeaderLine=2003
l_original_HeaderLine=Header line "{0}" can only occur once!
l_cause_HeaderLine=Each table based section MUST start with the corresponding header line. These header lines MUST only occur once in the document since each section also MUST only occur once.


l_code_NoHeaderLine=2004
l_original_NoHeaderLine=Current line "{0}" is a data line, the corresponding header line has not been defined yet.
l_cause_NoHeaderLine=Each table based section MUST start with the corresponding header line. These header lines MUST only occur once in the document since each section also MUST only occur once.


l_code_MsRunNotDefined=2005
l_original_MsRunNotDefined=Optional column header "{0}" ms_run[1-n] MUST be defined in the metadata section first.
l_cause_MsRunNotDefined=ms_run[1-n] MUST be defined in the metadata section first, before using it in an optional abundance column.


l_code_AssayNotDefined=2006
l_original_AssayNotDefined=Abundance optional column header "{0}" assay[1-n] MUST be defined in the metadata section first.
l_cause_AssayNotDefined=assay[1-n] MUST be defined in the metadata section first, before using it in an optional abundance column.


l_code_StudyVariableNotDefined=2007
l_original_StudyVariableNotDefined=Abundance optional column header "{0}": study_variable[1-n] MUST be defined in the metadata section first.
l_cause_StudyVariableNotDefined=study_variable[1-n] MUST be defined in the metadata section first, before using it in an optional abundance column.


l_code_NotDefineInMetadata=2008
l_original_NotDefineInMetadata="{0}" MUST be defined in the metadata section.
l_cause_NotDefineInMetadata=Elements specified as MANDATORY or MUST in the specification MUST be defined in the metadata section.


l_code_NotDefineInHeader=2009
l_original_NotDefineInHeader="{0}" MUST be defined in the header line of the "{1}" section.
l_cause_NotDefineInHeader= Elements specified as MANDATORY or MUST in the specification MUST be defined in their respective section.


l_code_DuplicationDefine=2010
l_original_DuplicationDefine="{0}" duplicate defined in the metadata section.
l_cause_DuplicationDefine=All non-indexed elements can only be defined once in the metadata section.


l_code_DuplicationAccession=2011
l_original_DuplicationAccession=DEPRECATED: Column "{0}" value "{1}" is a duplicate.
l_cause_DuplicationAccession=DEPRECATED: The accession of the protein in the source database. A protein accession MUST be unique within one mzTab file. If different quantification values are required for the same underlying accession, for example if differentially modified forms of a protein have been quantified, a suitable suffix SHOULD be appended to the accession.


l_code_AssayRefs=2012
l_original_AssayRefs="{0}" should be defined when assays and study variables are reported in the metadata section.
l_cause_AssayRefs=If both assays and study variables are reported in an mzTab file, the references to assays and study variables are MANDATORY.


l_code_ProteinCoverage=2013
l_original_ProteinCoverage=DEPRECATED: Column "{0}" value "{1}" is not a valid protein coverage value. It should be between 0 and 1.
l_cause_ProteinCoverage=DEPRECATED: A value between 0 and 1 defining the protein coverage


l_code_IdNumber=2014
l_original_IdNumber="{0}" id number "{1}" should be a number, and the value should be greater than 0.
l_cause_IdNumber=In mztab, multiple members are numbered 1..n, for example: Multiple sample processing are numbered sample_processing[1], sample_processing[2]


l_code_ModificationPosition=2015
l_original_ModificationPosition=DEPRECATED: Column "{0}" include a terminal modification "{1}", and its position must be between 0 and sequence "{2}".length + 1.
l_cause_ModificationPosition=DEPRECATED: Terminal modifications MUST be reported at position 0 or protein size + 1 respectively.


l_code_CHEMMODS=2016
l_original_CHEMMODS=DEPRECATED: Column "{0}" value "{1}" is kind of CHEMMODS. Their use is not recommended.
l_cause_CHEMMODS=DEPRECATED: For proteins and peptides, modifications SHOULD be reported using either UNIMOD or PSI-MOD. As these two ontologies/CVs are not applicable to small molecules, so-called CHEMMODs can also be defined. CHEMMODs MUST NOT be used if the modification can be reported using a PSI-MOD or UNIMOD accession.  Mass deltas MUST NOT be used for CHEMMODs if the delta can be expressed through a known chemical formula.


l_code_SubstituteIdentifier=2017
l_original_SubstituteIdentifier=DEPRECATED: Column "{0}" value "{1}" is not an original, unaltered amino acid sequence.
l_cause_SubstituteIdentifier=DEPRECATED: It is possible to report substitutions of amino acids using SUBST:{amino acid}. In these cases, the "sequence" column MUST contain the original, unaltered sequence.


l_code_SoftwareVersion=2018
l_original_SoftwareVersion=Software parameter "{0}" does not contain version information.
l_cause_SoftwareVersion=The parameter's value SHOULD contain the software's version. The order (numbering) should reflect the order in which the tools were used.


l_code_AbundanceColumnTogether=2019
l_original_AbundanceColumnTogether=Missing abundance column "{0}" in the header line.
l_cause_AbundanceColumnTogether=XXXX_abundance_study_variable[1-n], XXXX_abundance_variation_study_variable[1-n] should be displayed together, the order cannot change either.


l_code_AbundanceColumnSameId=2020
l_original_AbundanceColumnSameId=Abundance columns "{0}", "{1}", "{2}" study_variable id number should be the same.
l_cause_AbundanceColumnSameId=XXXX_abundance_study_variable[1-n], XXXX_abundance_variation_study_variable[1-n] should have the same study_variable[id] number.


l_code_SpectraRef=2021
l_original_SpectraRef=Column "{0}" value "{1}", "{2}" is "null". The use of "null" is allowed here however its use is discouraged.
l_cause_SpectraRef= If "spectra_ref" is present, the element "ms_run[1-n]-location" MUST be reported in the metadata section. Please check table 1 in the specification document.

l_code_AmbiguityMod=2022
l_original_AmbiguityMod=DEPRECATED: Column "{0}" value "{1}" represents Ambiguity of modification position at the Protein level. Ambiguity of modification position MUST NOT be reported at the Protein level.
l_cause_AmbiguityMod=DEPRECATED: Ambiguity of modification position MUST NOT be reported at the Protein level.


l_code_MsRunLocation=2023
l_original_MsRunLocation=DEPRECATED: "{0}" should be defined when assays are reported in the metadata section or if a PSM section is present in the file.
l_cause_MsRunLocation=DEPRECATED: If assays are reported or if a PSM section is present in the file, these attributes are MANDATORY, since back references to the MS run MUST be provided in certain sections. If the actual location of the MS run is unknown, a place holder value SHOULD be inserted.


l_code_FixedMod=2024
l_original_FixedMod=DEPRECATED: Fixed modifications are not defined in the metadata section.
l_cause_FixedMod=DEPRECATED: Fixed modifications should be defined in the metadata section, if PSM section is present.


l_code_VariableMod=2025
l_original_VariableMod=DEPRECATED: Variable modifications are not defined in the metadata section.
l_cause_VariableMod=DEPRECATED: Variable modifications should be defined in the metadata section, if PSM section is present.


l_code_PeptideSection=2026
l_original_PeptideSection=DEPRECATED: The existence of a Peptide Section line "{0}" is NOT RECOMMENDED in identification only files.
l_cause_PeptideSection= DEPRECATED: The existence of a Peptide section is NOT RECOMMENDED to be used in identification only files.


l_code_QuantificationAbundance=2027
l_original_QuantificationAbundance=DEPRECATED: If mzTab-type is "Quantification", then at least one section with {protein|peptide|small_molecule}_abundance* columns MUST be present
l_cause_QuantificationAbundance=DEPRECATED: If mzTab-type is "Quantification", then at least one section with {protein|peptide|small_molecule}_abundance* columns MUST be present


l_code_DuplicationID=2028
l_original_DuplicationID="{0}" contains duplicate identifier.
l_cause_DuplicationID=study_variable[1-n]-assay_refs and study_variable[1-n]-sample_refs MUST NOT contain duplicated identifier.


l_code_ProteinSearchEngineScoreNotDefined=2029
l_original_ProteinSearchEngineScoreNotDefined=Column header "{0}". protein_search_engine_score[1-n] should be defined in the metadata section first.
l_cause_ProteinSearchEngineScoreNotDefined=The best search engine score (for this type of score) for the given protein across all replicates reported. The type of score MUST be defined in the metadata section.

l_code_PeptideSearchEngineScoreNotDefined=2030
l_original_PeptideSearchEngineScoreNotDefined=Optional column header "{0}". peptide_search_engine_score[1-n] should be defined in the metadata section first.
l_cause_PeptideSearchEngineScoreNotDefined=The best search engine score (for this type of score) for the given protein across all replicates reported. The type of score MUST be defined in the metadata section.

l_code_PSMSearchEngineScoreNotDefined=2031
l_original_PSMSearchEngineScoreNotDefined=Optional column header "{0}". psm_search_engine_score[1-n] should be defined in the metadata section.
l_cause_PSMSearchEngineScoreNotDefined=The best search engine score (for this type of score) for the given protein across all replicates reported. The type of score MUST be defined in the metadata section.

l_code_SmallMoleculeSearchEngineScoreNotDefined=2032
l_original_SmallMoleculeSearchEngineScoreNotDefined=Optional column header "{0}". smallmolecule_search_engine_score[1-n] should be defined in the metadata section.
l_cause_SmallMoleculeSearchEngineScoreNotDefined=The best search engine score (for this type of score) for the given small molecule across all replicates reported. The type of score MUST be defined in the metadata section.

l_code_MsRunHashMethodNotDefined=2033
l_original_MsRunHashMethodNotDefined=ms_run[{0}]_hash is present, ms_run[{0}]_hash_method should be also present in the metadata section first.
l_cause_MsRunHashMethodNotDefined=If ms_run[1-n]-hash is present,  ms_run[1-n]-hash_method SHOULD also be present

l_code_ColumnNotValid=2034
l_original_ColumnNotValid=The column {0} is not a valid column for the section {1}.
l_cause_ColumnNotValid=The section contains a column that is not in the specification.

l_code_HeaderNotValid=2035
l_original_HeaderNotValid=The header in section {0} can not be parsed correctly.Items parsed "{1}", items count is "{2}"
l_cause_HeaderNotValid=The number of columns parsed is different that the number of columns.

l_code_NoSmallMoleculeSummarySection=2036
l_original_NoSmallMoleculeSummarySection=The mzTab file must contain a small molecule summary section.
l_cause_NoSmallMoleculeSummarySection=An mzTab file must contain at least one small molecule summary section.

l_code_NoSmallMoleculeFeatureSection=2037
l_original_NoSmallMoleculeFeatureSection=The mzTab file should contain a small molecule feature section.
l_cause_NoSmallMoleculeFeatureSection=An mzTab file should contain one small molecule feature section.

l_code_NoSmallMoleculeEvidenceSection=2038
l_original_NoSmallMoleculeEvidenceSection=The mzTab file should contain a small molecule evidence section.
l_cause_NoSmallMoleculeEvidenceSection=An mzTab file should contain one small molecule evidence section.

l_code_NoSmallMoleculeQuantificationUnit=2039
l_original_NoSmallMoleculeQuantificationUnit=The metadata section must contain a small_molecule-quantification_unit parameter definition.
l_cause_NoSmallMoleculeQuantificationUnit=The metadata section must contain a small_molecule-quantification_unit parameter definition for small molecule abundances.

l_code_NoSmallMoleculeFeatureQuantificationUnit=2040
l_original_NoSmallMoleculeFeatureQuantificationUnit=The metadata section must contain a small_molecule_feature-quantification_unit parameter definition.
l_cause_NoSmallMoleculeFeatureQuantificationUnit=The metadata section must contain a small_molecule_feature-quantification_unit parameter definition for small molecule feature abundances.

l_code_NoSmallMoleculeIdentificationReliability=2041
l_original_NoSmallMoleculeIdentificationReliability=The metadata section should contain a small_molecule-identification_reliability parameter definition.
l_cause_NoSmallMoleculeIdentificationReliability=The metadata section should contain a small_molecule-identification_reliability parameter definition for reporting of small molecule identification reliability.

l_code_ExternalStudyIdFormatNotDefined=2042
l_original_ExternalStudyIdFormatNotDefined="{0}": id_format parameter must be defined for external study.
l_cause_ExternalStudyIdFormatNotDefined=If an external study is defined in the metadata section, it must also define the id_format parameter.

l_code_ExternalStudyFormatNotDefined=2043
l_original_ExternalStudyFormatNotDefined="{0}": format parameter must be defined for external study.
l_cause_ExternalStudyFormatNotDefined=If an external study is defined in the metadata section, it must also define the id_format parameter.

l_code_NoDatabaseMustHaveNullPrefix=2044
l_original_NoDatabaseMustHaveNullPrefix="The prefix for database[{0}] with name "no database" must be "null" but it was "{1}".
l_cause_NoDatabaseMustHaveNullPrefix=The prefix used in the "identifier" column of data tables. For the "no database" case "null" must be used.

l_code_NoMetadataSection=2045
l_original_NoMetadataSection=The mzTab file MUST contain a metadata section.
l_cause_NoMetadataSection=An mzTab file MUST contain a metadata section.

l_code_ItemNumberMismatch=2046
l_original_ItemNumberMismatch=The attribute list "{0}" with "{1}" items must hold the same number of items as the attribute list "{2}" which has "{3}" items.
l_cause_ItemNumberMismatch=Attributes that may report lists of properties, e.g. database_identifier can impose a constraint on the length of other attribute lists related to the same element, e.g. chemical_formula.

l_code_UnknownRefId=2047
l_original_UnknownRefId=Reference id "{0}" for column "{1}" from element "{2}" in section "{3}" to section "{4}" must have a matching element defined.
l_cause_UnknownRefId=Reference ids within mzTab MUST reference existing objects. A reference MUST not be null and MUST not point to an undefined object.

l_code_SingleStudyVariableName=2048
l_original_SingleStudyVariableName=A single study variable MUST be reported with identifier "undefined". It must link to all assays.
l_cause_SingleStudyVariableName=For software that does not capture study variables, a single study variable MUST be reported, linking to all assays. This single study variable MUST have the identifier "undefined".

l_code_UndefinedStudyVariableNameOnceOnly=2049
l_original_UndefinedStudyVariableNameOnceOnly="{0}" MUST not use the identifier "undefined". This value MUST only be used when reporting a single unspecified study variable within the mzTab file.
l_cause_UndefinedStudyVariableNameOnceOnly=For software that does not capture study variables, a single study variable MUST be reported, linking to all assays. This single study variable MUST have the identifier "undefined".

l_code_SpectraIdFormatNotValid=2050
l_original_SpectraIdFormatNotValid=The spectra_ref element "{0}" for column "{1}" must follow the defined ms_run[1-n]-id_format pattern "{2}".
l_cause_SpectraIdFormatNotValid=If "spectra_ref" is present, the reference must follow the CV term format defined in ms_run[1-n]-id_format. Please check table 1 in the specification document.

l_code_SpectraIdFormatNotSupported=2051
l_original_SpectraIdFormatNotSupported=The spectra_ref element "{0}" for column "{1}" uses an ms_run[1-n]-id_format not supported by the validator.
l_cause_SpectraIdFormatNotSupported=The CV term defined in ms_run[1-n]-id_format is currently unsupported by the validator. Please contact the reference validator team at https://github.com/lifs-tools/jmzTab-m to add support for it.