Last updated:2016.3.22.

validator error message

In this site, error messages outputted from checking tools for nucleotide sequence data submission are briefly explained.
If you find any error message, please make some appropriate correction.
If you have any problems and/or questions, please contact us with error messages.

 

List of Parser error messages

In this section, brief explanations for Parser error messages are shown in the code number order.
See format of error messages at Format of Parser outputs.
When an error is occured, it is required to be resolved by modification of files, in principle.
If you have any problems and/or questions, please contact us with error messages.

Terms and numbers closed with brackets ( [ and ] ) and started from #, are substituted by each real value that is used in your submission.

Terms closed with brackets ( [ and ] ) and not started from # are the reserved words for features or qualifiers.

You can search explanations for parser error messages by selecting from the following box;


JP0001
Format
JP0001:FAT:SYS: Internal error occurred.
Description
The internal error is detected.

JP0002
Format
JP0002:ER1:SYS: System file read error. [#FILE NAME]
Description
Some error is occurred, when the system is reading the file.

JP0003
Format
JP0003:ER1:SYS: [#FILE NAME] cannot be opened.
Description
The system file cannot be opened. Please reinstall the system.

JP0005
Format
JP0005:ER1:SYS:ANN: Ambiguous annotation file specification [#FILE NAME1] <=> [#FILE NAME2].
Description
Annotation file cannot be specified. Please specify the one annotation file.

JP0006
Format
JP0006:ER1:SYS:SEQ: Ambiguous sequence file specification [#FILE NAME1] <=> [#FILE NAME2].
Description
Sequence file cannot be specified. Please specify the one sequence file.

JP0007
Format
JP0007:ER1:SYS: Invalid parameter specification: [#PARAMETER]
Description
Please check the parameter that is specified invalidly.

JP0008
Format
JP0008:MES:SYS: Usage : ... [-x<annotation file>] [-s<sequence file>]
Description
Please specify the parameter as the following format; [-x<annotation file>] [-s<sequence file>]

JP0009
Format
JP0009:ER1:STX:AxS: Numbers of entries are different between sequence file ([#N1]) and annotation file ([#N2]).
Description
The number of entries in the sequence file is different from that in the annotation file.
Please unify the number of entries.

JP0011
Format
JP0011:ER1:STX:AxS:Line [#N1] in annotation file: [#ENTRY NAME1] does not match with [#ENTRY NAME2] at Line [#N2] in sequence file.
Description
The entry name in the annotation file is different from that in the sequence file.
It is required to sort entries in the same order for both annotation and sequence files.

JP0012
Format
JP0012:MES:STX:SEQ:Line [#N]: Extra information is included in entry name: [#ENTRY NAME].
Description
In the sequence file, some extra information is found in the entry line.
Please confirm and re-enter the entry name again, if necessary.

JP0013
Format
JP0013:ER1:STX:SEQ:Line [#N]: Entry line is not found.
Description
In the sequence file, there is no entry line. Please enter the entry name.

JP0014
Format
JP0014:ER1:STX:SEQ:Line [#N1]: Invalid code [#LETTER] at [#N2]-th letter.
Description
In the sequence file, an invalid code is found. Please correct the nucleotide code.
See the acceptable nucleotide codes.

JP0015
Format
JP0015:ER1:STX:SEQ:Line [#N]: Sequence is not terminated by [ // ].
Description
In the sequence file, the termination code for the sequence, "//" is not found.
Please enter the code "//" for the end of sequence.

JP0016
Format
JP0016:ER1:STX:SEQ:Lines [#N1] and [#N2]: entry name [#ENTRY NAME] is same.
Description
In the sequence file, the entry name is found two or more times. Please correct them to be unique.

JP0017
Format
JP0017:ER1:STX:ANN:Lines [#N1] and [#N2]: entry name [#ENTRY NAME] is same.
Description
In the annotation file, the entry name is found two or more times. Please correct them to be unique.

JP0019
Format
JP0019:ER1:STX:ANN:Line [#N]: The number of columns is greater than 5.
Description
In the annotation file, you entered 6 or more columns in the line. Please delete the illegal column(s).
The number of acceptable columns is five; for Entry, Feature, Location, Qualifier and Value, respectively.

JP0020
Format
JP0020:ER1:STX:ANN:Line [#N]: Over flow (max: 40959 bytes/line).
Description
The number of characters is greater than 40959 bytes/line that is the maximum for a line.

JP0021
Format
JP0021:ER1:STX:ANN:Entry [#ENTRY NAME]: [#FEATURE NAME] feature is required for an entry.
Description
The following features are required at least one for COMMON or each of entries;
SUBMITTER, REFERENCE and source

JP0022
Format
JP0022:ER1:STX:ANN:Line [#N]: Entry name is not appropriate.
Description
Null and/or illegal characters are found in the entry name.

JP0023
Format
JP0023:ER1:STX:ANN:Line [#N]: Feature is undefined.
Description
No feature is specified. Please use some appropriate feature.

JP0024
Format
JP0024:ER1:STX:ANN:Line [#N]: [#FEATURE NAME] feature must be described in the [ COMMON ] entry.
Description
DATE and DATATAPE feature can be only entered in the COMMON entry.

JP0025
Format
JP0025:ER1:STX:ANN:Line [#N]: Location is required.
Description
The location is not specified for a biological feature. Please describe some appropriate location.

JP0026
Format
JP0026:ER1:STX:ANN:Line [#N]: Unrecognizable/forbidden feature [#FEATURE NAME] is found.
Description
An invalid name for feature is found.
Please note frequently mistyped cases as follows;
1) case sensitivity, to distinguish upper or lower case;
2) missing the underscore character, "_";
i.e. "TRNA" --> "tRNA" ; "misc feature" --> "misc_feature"

JP0027
Format
JP0027:ER1:STX:ANN:Line [#N]: Unrecognizable/forbidden qualifier name [#QUALIFIER NAME] is found.
Description
An invalid name for qualifier is found.
Please note frequently mistyped cases as follows;
1) the case sensitivity, to distinguish upper or lower case;
2) missing the underscore character, "_";
i.e. "Codon start" --> "codon_start"

JP0029
Format
JP0029:ER2:STX:ANN:Entry [#ENTRY NAME]: Without keyword [#KEYWORD VALUE], though the [ DATATYPE/type ] is [#TYPE VALUE].
Description
DATATYPE/type is specified, the required keyword corresponding to the type is not found.

JP0031
Format
JP0031:ER1:STX:ANN:Line [#N]: [#FEATURE NAME] feature must have [#QUALIFIER NAME1] or [#QUALIFIER NAME2] qualifier.
Description
Either one of two qualifiers is required for the feature. Please specify one of them.

JP0032
Format
JP0032:ER1:STX:ANN:Lines [#N1] and [#N2]: 2 or more [#FEATURE NAME] features are found in an entry.
Description
The feature can be used only one for one entry.

JP0033
Format
JP0033:ER1:STX:ANN:Lines [#N1] and [#N2]: [ Published Only in Database ] status must be used in the 1st REFERENCE.
Description
The value for the status qualifier, "Published Only in Database" can only be described for the first REFERENCE feature of the entry.

JP0034
Format
JP0034:ER1:STX:ANN:Lines [#N1] and [#N2]: [ Published Only in Database ] status qualifiers is found 2 times in an entry, [#ENTRY NAME].
Description
There are two or more values, "Published Only in Database" in the entry.
Please specify the status, "Published Only in Database", for the only 1st REFERENCE feature of the entry.

JP0035
Format
JP0035:ER2:STX:ANN:Line [#N]: One of [ ab_name ] values must be corresponding to the value of [contact].
Description
There is no ab_name qualifier with the value corresponding to the value of the contact qualifier.

JP0036
Format
JP0036:ER1:STX:ANN:Line [#N]: [#STATUS VALUE] status can NOT be used with [#QUALIFIER NAME] qualifier.
Description
Invalid qualifier is described in REFERENCE with a specified status. Please correct it.

JP0037
Format
JP0037:MES:STX:ANN:Line [#N]: [#ENTRY NAME] entry: Location of [#FEATURE NAME] feature is meaningless.
Description
The descriptions of the locations are ignored for the following features; SUBMITTER, REFERENCE and COMMENT.
When the number of REFERENCE or COMMENT features is plural, the order of the features in the annotation file is to be same with the order in the flat file.

JP0038
Format
JP0038:WAR:STX:SEQ:Entry [#ENTRY NAME]: Length ([#N] bp) of sequence seems too short, it should be greater than 20 bp.
Description
In principle, the acceptable length of sequence is more than 20bp.
Please confirm it again, if necessary.

JP0039
Format
JP0039:ER1:LOC:AxS:Entry [#ENTRY NAME]: The location of [ source ] feature is greater than the sequence length in sequence file by [#N] bp.
Description
The range of the location of source feature is greater than the sequence length in the sequence file.
Please correct the sequence and/or the description of the location.

JP0040
Format
JP0040:ER2:LOC:AxS:Entry [#ENTRY NAME]: The sequence length in sequence file is greater than the location of [ source ] feature(s) by [#N] bp.
Description
The sequence length in the sequence file is greater than all ranges of source locations.
Please correct the sequence and/or the description of location.

JP0041
Format
JP0041:WAR:LOC:ANN:Line [#N]: The [ source ] feature with single location is not found.
Description
The description of location for source feature may be invalid.
Please confirm the sequence and the description of the location again and revise them, if necessary.

JP0042
Format
JP0042:WAR:STX:ANN:Line [#N]: The [ source ] feature with maximum span does not start from 1.
Description
The longest location of the source features is not started from 1.
Please confirm the location again and revise it, if necessary.

JP0043
Format
JP0043:WAR:STX:SEQ:Line [#N]: First code of sequence is [ n ], it should be trimmed.
Description
The first base code of the sequence is "n".
Please remove it, because the first nucleotide should not be "n".

JP0044
Format
JP0044:WAR:STX:SEQ:Line [#N]: Last code of sequence is [ n ], is should be trimmed.
Description
The last base code of the sequence is "n".
Please remove it, because the last nucleotide should not be "n".

JP0045
Format
JP0045:ER1:LOC:AxS:Line [#N] in annotation file: [#ENTRY NAME]: [#FEATURE NAME] [#LOCATION VALUE] contains some base code other than [ n ] in sequence file.
Description
In the sequence file, the base code other than "n" is found at the location of gap or assembly_gap feature specified in the annotation file.

JP0046
Format
JP0046:WAR:LOC:AxS:Entry [#ENTRY NAME]: [#LOCATION VALUE] is consist of base code [#N] x [ n ], without corresponding [ gap or assembly_gap ] feature.
Description
In the sequence file, the location that is greater than 10 in the length consists of the only base code, "n", however, there is neither gap or assembly_gap feature corresponding to the location in the annotation file.

JP0047
Format
JP0047:ER1:STX:ANN:Line [#N]: [#ENTRY NAME]: [#FEATURE NAME] [#LOCATION VALUE], the location is invalid.
Description
The location of unsure, gap or assembly_gap feature is invalid.
Any operators, "join", "order" or "complement" are not acceptable for the location of unsure, gap or assembly_gap feature.

JP0053
Format
JP0053:ER2:STX:ANN:Lines [#N1] and [#N2]: values of [ mol_type ] qualifier are different in an entry [#ENTRY NAME].
Description
In an entry with two or more source features, each mol_type qualifier must have the same value.
Please unify them with the same values.

JP0054
Format
JP0054:ER1:STX:ANN:Entry [#ENTRY NAME]: One of [ source ] feature with DIFFERENT [ organism ] qualifiers is required [ focus ] or [ transgenic ] qualifier.
Description
Either focus or transgenic is required for the qualifier in either of the source features, when two or more source features in an entry with the different values of organism qualifiers.

JP0056
Format
JP0056:ER1:STX:ANN:Line [#N]: [#QUALIFIER NAME] qualifier must be removed.
Description
Please delete the qualifier (focus or transgenic) from the source feature.
It can be only used to specify the main source from two or more source features.

JP0058
Format
JP0058:ER1:STX:ANN:Line [#N]: [ source ] features with the SAME [ organism ] qualifiers can NOT have [ focus ] qualifier in an entry [#ENTRY NAME].
Description
When there are some source features and all of them have the same organism qualifier, the focus qualifier cannot be used.

JP0059
Format
JP0059:ER1:STX:ANN:Lines [#N1] and [#N2]: [ transgenic ] qualifiers are found in an entry [#ENTRY NAME].
Description
2 or more transgenic qualifiers are found in the entry.
Only one transgenic qualifier can be used for an entry.
Please remove them except either one in the main source feature.

JP0060
Format
JP0060:ER1:STX:ANN:Line [#N]: [ transgenic ] qualifier can be used for only [ SYN ] division.
Description
The transgenic qualifier can be only used for the entry of "SYN" division.

JP0061
Format
JP0061:ER2:STX:ANN:Line [#N]: Without [ environmental_sample ] qualifier in [ source ] feature, though it is [ ENV ] division.
Description
The division of the entry is "ENV", however, there is no environmental_sample qualifier in the source feature.

JP0062
Format
JP0062:ER2:STX:ANN:Line [#N]: Without keyword [ ENV ], though [ environmental_sample ] qualifier is used.
Description
The environmental_sample qualifier is used for the entry, however, 'ENV' is not found in the value of the keyword qualifier.

JP0063
Format
JP0063:WAR:STX:ANN:Line [#N]: Without division [ ENV ], though [ environmental_sample ] qualifier is used.
Description
The division is not specified as "ENV", though the environmental_sample qualifier is used.

JP0064
Format
JP0064:ER1:LOC:ANN:Line [#N]: [#ENTRY NAME]: [#FEATURE NAME] feature can NOT refer other entry.
Description
The feature cannot refer any other entry for its location.
This rule is applied to operon and other relevant features belonging to the operon transcript.

JP0065
Format
JP0065:WAR:LOC:ANN:Line [#N]: [#ENTRY NAME]: [#FEATURE NAME] feature [#LOCATION VALUE1] is overlapped with [ operon ] feature [#LOCATION VALUVE2].
Description
The location of the feature is overlapped with that of some operon feature.
Please add the common operon qualifiers for both features, if necessary.

JP0066
Format
JP0066:ER2:STX:ANN:Line [#N1]: [#ENTRY NAME]: [#FEATURE NAME] feature [#LOCATION VALUE] should have the same [ operon ] qualifier that is used for the [ operon ] feature at line [#N2].
Description
The feature has an operon qualifier, but there is no operon feature that has the same operon qualifier in its value.
Please check the values of operon qualifiers.

JP0067
Format
JP0067:ER2:STX:ANN:Line [#N]: [#ENTRY NAME]: [ operon ] feature should have at least one related feature.
Description
To describe the operon feature, at least one another feature related to the operon is required.

JP0068
Format
JP0068:ER2:STX:ANN:Line [#N]: [#ENTRY NAME]: [#FEATURE NAME] feature has [ operon ] qualifier, though it is NOT overlapped with any [ operon ] feature.
Description
The feature has an operon qualifier, but it is not overlapped with any operon feature in its location.

JP0070
Format
JP0070:ER1:STX:ANN:Lines [#N1] and [#N2]: [ ff_definition ] qualifiers are found in an entry [#ENTRY NAME].
Description
2 or more ff_definition qualifiers are found in the entry.
Only one ff_definition qualifier can be used for an entry. Please remove them except either one.

JP0072
Format
JP0072:ER1:LOC:ANN:Line [#N]: Location [#LOCATION VALUE] is invalid.
Description
The description of location is invalid. Please correct according to Description of Location.

JP0073
Format
JP0073:ER1:STX:ANN:Line [#N]: [#QUALIFIER NAME] qualifier can NOT use for [#FEATURE NAME] feature.
Description
The qualifier is not legal for the feature.
Please correct according to Feature/Qualifier Usage Matrix

JP0074
Format
JP0074:ER1:STX:ANN:Line [#N]: [#QUALIFIER NAME] qualifier is required for [#FEATURE NAME] feature.
Description
The mandatory qualifier for the feature is not found.
Please correct according to Feature/Qualifier Usage Matrix

JP0075
Format
JP0075:ER1:STX:ANN:Line [#N]: Invalid value [#VALUE] for [#QUALIFIER NAME] qualifier, it must be modified following [#VALUE_CONDITION].
Description
The value for the qualifier is invalid. Please revise the value.

JP0077
Format
JP0077:ER1:STX:ANN:Line [#N]: Invalid char [#VALUE] for [#QUALIFIER NAME] qualifier, it must be modified following [#CHAR_CONDITION].
Description
The value for the qualifier is not described with the prescribed characters. Please revise the value.

JP0078
Format
JP0078:ER1:STX:ANN:Line [#N]: Invalid length [#VALUE] for [#QUALIFIER NAME] qualifier, it must be modified following [#LENGTH_CONDITION].
Description
The value for the qualifier is not described in the prescribed length. Please revise the value.

JP0079
Format
JP0079:ER2:STX:ANN:Line [#N]: The value of [ experiment ] qualifier is recommended to be less than 1000 letters.
Description
The value of experiment qualifier is recommended to be less than 1000 in the number of letters.

JP0080
Format
JP0080:WAR:STX:ANN:Lines [#N1] and [#N2]: Feature [#FEATURE NAME] [#LOCATION VALUE] is duplicated in the entry [#ENTRY NAME].
NAME].
Description
Please correct the duplication of the feature in the entry, if necessary.

JP0081
Format
JP0081:WAR:LOC:ANN:Line [#N]: Location [#LOCATION VALUE] should be merged.
Description
In the description of the location, the pieces of "join" or "order" can be merged each other.
i.e. "join(1..100,101..200)" → "1..200"

JP0082
Format
JP0082:WAR:LOC:ANN:Line [#N]: Location [#LOCATION VALUE] is possibly overlapped.
Description
In the description of the location, the pieces of "join" or "order" are overlapped with each other.
i.e. "join(1..100,50..200)"

JP0083
Format
JP0083:ER1:STX:ANN:Line [#N]: To use [#QUALIFIER NAME1] qualifier, [#QUALIFIER NAME2] qualifier is required in the [#FEATURE NAME] feature.
Description
When the [#QUALIFIER NAME1] qualifier is used for the feature, the [#QUALIFIER NAME2] qualifier is required.

JP0085
Format
JP0085:WAR:STX:ANN:Line [#N]: No qualifier is found after specified location column.
Description
No qualifier is described, though the location is described in the line.

JP0086
Format
JP0086:ER2:STX:ANN:Entry [#ENTRY NAME]: EST entry must have one of these 3 terms; [ unspecified EST ], [ 5'-end sequence (5'-EST) ] or [ 3'-end sequence (3'-EST) ] in its keyword.
Description
For EST entries, either of three following keywords is required;
"unspecified EST", "5'-end sequence (5'-EST)" or "3'-end sequence (3'-EST)"

JP0087
Format
JP0087:ER2:STX:ANN:Entry [#ENTRY NAME]: TPA entry must have one of these 2 terms; [ TPA: experimental ] or [ TPA:inferential ] in its keyword.
Description
For TPA entry, either of the following two keywords is required; "TPA:experimental" or "TPA:inferential"

JP0088
Format
JP0088:ER1:STX:ANN:Lines [#N1] and [#N2]: [#QUALIFIER NAME] qualifier [#VALUE] is duplicated at [#FEATURE NAME] feature.
Description
The qualifier is duplicated in the same feature. Please confirm and correct them.

JP0103
Format
JP0103:WAR:STX:ANN:Line [#N]: [#QUALIFIER VALUE] has '@' which doesn't construct meta characters.
Description
There are some '@' letters that do not contribute to the meta-description in the value of qualifier which is allowed to use meta-description.

JP0104
Format
JP0104:WAR:STX:ANN:Line [#N]: '[#ELEMENT]' of [#QUALIFIER NAME] isn't valid meta character format.
Description
In the value of qualifier, there is a description similar to the meta-description of '[qualifier name or entry]'.

JP0105
Format
JP0105:WAR:STX:ANN:Line [#N]: [#QUALIFIER NAME] doesn't have a value, though it is referred by [ ff_definition ].
Description
There is no value for the qualifier specified by the meta-description in the "ff_definition".

JP0106
Format
JP0106:ER1:STX:AxS:Entry [#ENTRY NAME1] and [#ENTRY NAME2]: Order of entry in annotation file is different from that in sequence file.
Description
The orders of entries in annotation and sequence files are different from each other.

JP0107
Format
JP0107:ER1:STX:AxS:Entry [#ENTRY NAME]: Not found in fasta file.
Description
The entry name is found in the annotation file, however, it is not found in the sequence file.

JP0108
Format
JP0108:ER1:STX:ANN:Lines [#N1] and [#N2]: The keyword [#VALUE] duplicated at the entry [#ENTRY NAME].
Description
The same keyword is found two times in the entry.

JP0109
Format
JP0109:ER2:STX:ANN:Line [#N]: Usage of ambiguous or particular AA residue is problematic for [#QUALIFIER NAME] qualifier.
Description
Since the amino acid abbreviation in the qualifier is ambiguous (Asx, Glx, or Xle) or particular (Sec or Pyl), it would cause some problem.

JP0110
Format
JP0110:ER2:STX:ANN:Entry [#ENTRY NAME]: Without keyword [#KEYWORD VALUE], though the [ DIVISION/division ] is [#DIVISION VALUE].
Description
There is no keyword that is required for the specified DIVISION/division.

JP0111
Format
JP0111:ER2:STX:ANN:Entry [#ENTRY NAME]: [ DIVISION/division ] [#DIVISION VALUE] is not specified, though the specific keyword [#KEYWORD VALUE] is found.
Description
The given keyword is specific to some DIVISION/division, however, the DIVISION/division is not specified.

JP0112
Format
JP0112:WAR:LOC:AxS:Entry [#ENTRY NAME]: [#LOCATION VALUE1] is consist of base code [#N] x [ n ], it is longer than corresponding [ gap or assembly_gap ] feature at [#LOCATION VALUE2].
Description
In the sequence file, the location that is greater than 10 in the length consists of the only base code, "n", however, the corresponding gap or assembly_gap feature indicates different location in the annotation file.
Please modify sequence file and/or annotation file to resolve this disagreement.

JP0113
Format
JP0113:ER1:STX:ANN:Line [#N]: Value of [ codon_start ] is not 1, but [#LOCATION VALUE] is 5' complete type.
Description
When the value of codon_start is not 1, the location value must be 5' partial type.
Please check the frame of translated amino acid sequence for the corresponding CDS feature.
Please correct either of them, according to Description of Location and Offset of the frame at translation initiation by /codon_start.

JP0114
Format
JP0114:WAR:STX:ANN:Line [#N]: The value format of [ ab_name ] [#VALUE] is possibly wrong.
Description
The value of ab_name has possibly format error. Please reconfirm it, and, if necessary, correct it.

JP0115
Format
JP0115:WAR:STX:ANN:Lines [#N1] and [#N2]: [ ab_name ] [#VALUE] is duplicated in [SUBMITTER/REFERENCE].
Description
The same ab_name is found two times in a feature SUBMITTER or REFERENCE.
Please reconfirm it, and, if necessary, correct it.

JP0116
Format
JP0116:ER2:STX:ANN:Line [#N]: Invalid format [#VALUE] for [#QUALIFIER NAME] qualifier, it must be modified following [#FORMAT_CONDITION].
Description
The value for the qualifier is not described in the prescribed format. Please revise the value.

JP0117
Format
JP0117:ER2:STX:ANN:Line [#N]: Both [#QUALIFIER NAME1] and [#QUALIFIER NAME2] qualifiers are found.
Description
Please remove either one of two qualifiers, because both of two cannot be used in the same feature.

JP0118
Format
JP0118:ER1:SYS: Option [-b] is invalid, this option is specific to CONTIG.
Description
When you specify the option "-b", it is required to specify the CON division in annotation file.

JP0119
Format
JP0119:WAR:STX:ANN:Line [#N]: Some character other than [ 0-9 ] is found in [#VALUE] for [#QUALIFIER NAME].
Description
The value for volume, start_page, end_page qualifier is usually described in only numeric character.
Please reconfirm it, and, if necessary, correct it.

JP0120
Format
JP0120:FAT:SYS: Out of memory error occurred.
Description
There is insufficient memory. Please allocate memory.

JP0121
Format
JP0121:ER1:STX:ANN:Line [#N]: [ COMMON ] must be used for the first entry to describe features shared with all entries.
Description
The symbolic entry name, COMMON, can be used only in the first of your entries, when you need to specify
features shared with all of entries in the COMMON entry.
If the following description is entered on the first line, please remove the line.
e.g.) Entry Feature Location Qualifier Value

JP0122
Format
JP0122:ER1:STX:ANN:Lines [#N1] and [#N2]: 2 or more [#QUALIFIER NAME] qualifiers are found in [#FEATURE NAME] feature.
Description
2 or more qualifiers are found in the feature, however, the qualifier can be specified only one for the feature.
Please delete one of them.

JP0123
Format
JP0123:ER1:STX:ANN:Line [#N]: [#LOCATION VALUE] is including invalid character(s).
Description
Location includes some invalid character(s). Please revise the location.

JP0124
Format
JP0124:ER1:STX:ANN:Line [#N]: Value of [#QUALIFIER NAME] qualifier has invalid Head/End space.
Description
In the beginning or the end of value, extra space(s) is found. Please remove it.

JP0125
Format
JP0125:ER2:STX:ANN:Lines [#N1] and [#N2]: 2 or more [#QUALIFIER NAME] qualifiers are found in [#FEATURE NAME] feature.
Description
2 or more qualifiers are found in the feature, however, the qualifier can be specified only one for the feature.
Please change one of them into another qualifier (e.g. note qualifier).

JP0126
Format
JP0126:WAR:STX:ANN:Line [#N]: [#QUALIFIER NAME] qualifier value has [#N] invalid 2 or more consecutive spaces.
Description
2 or more consecutive spaces are found in the value. Please remove extra space(s).

JP0127
Format
JP0127:ER1:STX:ANN: CON division mixed with other ones.
Description
An entry in the CON division can not be with any entries in other divisions in an annotation file.
Please divide the entries into two or more submission files, if necessary.

JP0128
Format
JP0128:ER1:STX:ANN:Line [#N]: [#ENTRY NAME] for entry name is too long, it must be shorter than 33 letters.
Description
Entry name is too long. Please describe it in less than 33 letters of characters.

JP0129
Format
JP0129:ER1:STX:ANN:Line [#N]: [#ENTRY NAME] is invalid for entry name, do not use space, back-slash or double-quote.
Description
Entry name has invalid character(s) ( [space], " [double-quote], ? [question], \ [back-slash]).
Please remove them.

JP0130
Format
JP0130:WAR:STX:ANN:Line [#N]: End of value is comma in [#QUALIFIER NAME] qualifier.
Description
A comma is found at the end of the value.

JP0131
Format
JP0131:WAR:LOC:ANN:Lines [#N1] and [#N2]: Multi source locations [#LOCATION VALUE1] and [#LOCATION VALUE2] may overlap mutually.
Description
The locations of two source features are possibly overlapping each other.
Please reconfirm it, and, if necessary, correct it.

JP0132
Format
JP0132:ER1:STX:ANN:Line [#N]: Meta character @@[#ELEMENT]@@ is duplicated in [#QUALIFIER NAME] qualifier.
Description
The same meta-description is found two or more times in the value of qualifier.

JP0133
Format
JP0133:ER1:STX:ANN:Line [#N]: Meta character @@[#ELEMENT]@@ can NOT be used in [#QUALIFIER NAME] qualifier.
Description
Invalid meta-description is found in the value of the specified qualifier.

JP0134
Format
JP0134:WAR:STX:ANN:Line [#N]: Meta character @@[organism]@@ must be set at the beginning of [ ff_definition ] qualifier.
Description
Only "organism" qualifier can be specified by meta-description at the beginning of the value of the "ff_definition" qualifier.

JP0135
Format
JP0135:WAR:STX:ANN:Line [#N]: There is no space at the right of meta character @@[organism]@@ in [ ff_definition ] qualifier.
Description
Please insert a space after "@@[organism]@@".

JP0136
Format
JP0136:WAR:STX:ANN:Line [#N]: Meta character @@[#ELEMENT]@@ is not delimited by the space or comma-space.
Description
Except for "@@[organism]@@", please insert a space before meta-description, and insert a space or a comma-space after meta-description.

JP0137
Format
JP0137:WAR:STX:ANN:Entry [#ENTRY NAME]: TSA entry should have [#FEATURE NAME] feature.
Description
Specified feature should be described for TSA entry.

JP0138
Format
JP0138:ER1:STX:ANN:Line [#N]: Both [ start_page ] and [ end_page ] qualifiers must be specified.
Description
Both "start_page" and "end_page" are not described.
If the reference is a one-page article, please input the same page number in both "start_page" and "end_page".

JP0144
Format
JP0144:ER1:STX:ANN:Line [#N]: [ volume ] is not found, but [ start_page ] and [ end_page ] qualifiers are specified.
Description
No volume qualifier is described, though the "start_page" and "end_page" qualifiers are described in REFERENCE. Please input it.

JP0145
Format
JP0145:WAR:STX:ANN:Line [#N]: [#QUALIFIER NAME] qualifier is ignored because of [#STATUS VALUE] status.
Description
Nonsense qualifier is described in REFERENCE with a specified status.

JP0146
Format
JP0146:ER1:STX:ANN:Line [#N]: [ end_page ] value is less than [ start_page ].
Description
The value of "end_page" is less than that of "start_page". Please correct it.

JP0147
Format
JP0147:WAR:STX:ANN:Line [#N]: Values of [ start_page ] and [ end_page ] are same.
Description
The values of start_page and end_page are the same.
If the reference is a one-page article, please ignore the message.

JP0148
Format
JP0148:ER1:LOC:ANN:Line [#N]: The number of location [#NUMBER] starts with 0.
Description
A base number in location should not have leading zeros. Please remove them.
i.e. "01..100", "1..0100" --> "1..100"

JP0149
Format
JP0149:WAR:STX:ANN:Line [#N]: hold_date [#VALUE] is too near.
Description
The 'hold_date' is specified within 10 days.
We recommend you specify the date with enough time (e.g. six month later).
If your data should be open to public immediately, please delete DATE line.

JP0150
Format
JP0150:WAR:STX:ANN:Line [#N]: keyword [#VALUE] is not defined in standard list.
Description
Please select keyword defined in standard list.

JP0151
Format
JP0151:ER2:STX:ANN:Line [#N]: Both keyowords [ TPA:experimental ] and [ TPA: inferential ] are found.
Description
For TPA entry, either of the following two keywords is required; "TPA:experimental" or "TPA:inferential".
Please delete either one of the two.

JP0152
Format
JP0152:ER1:STX:ANN:Line [#N]: [#VALUE] for [#QUALIFIER NAME] qualifier must be includes in [#LOCATION_VALUE].
Description
For anticodon, rpt_unit_range, tag_peptide and transl_except qualifier, their position must be located within each Feature location.

JP0154
Format
JP0154:ER1:STX:ANN:Line [#N]: Invalid length [#QUALIFIER NAME] qualifier in [ ST_COMMENT ] feature, it must be modified following [#LENGTH_CONDITION].
[#LENGTH_CONDITION].
Description
Qualifier in ST_COMMENT feature is too long. Please describe it in less than 64 letters of characters.

JP0155
Format
JP0155:ER1:STX:ANN:Line [#N]: Invalid char [#QUALIFIER NAME] qualifier in [ ST_COMMENT ] feature, it must be modified following [#CHAR_CONDITION].
[#CHAR_CONDITION].
Description
Qualifier in ST_COMMENT feature has invalid character(s). Please remove them.

JP0156
Format
JP0156:ER1:STX:ANN:Line [#N]: Invalid [#QUALIFIER NAME] qualifier in [ ST_COMMENT ] feature, it must be modified following [ can't use [@@&&,::] ].
Description
You can't use "@@&&,::" in Qualifier in ST_COMMENT feature (except tagset_id qualifier).

JP0157
Format
JP0157:WAR:STX:ANN:Line [#N]: There is no value for [#QUALIFIER NAME] qualifier in [ ST_COMMENT ] feature.
Description
There is no value for the qualifier in ST_COMMENT. Please enter the value, if necessary.

JP0158
Format
JP0158:ER1:STX:ANN:Line [#N]: [ tagset_id ] qualifier must be set at the beginning of [ ST_COMMENT ] feature.
Description
The tagset_id qualifier must be set at the beginning of ST_COMMENT feature.

JP0159
Format
JP0159:ER1:STX:ANN:Lines [#N1] and [#N2]: 2 or more [ tagset_id ] qualifiers with [#VALUE] are found in an entry [#ENTRY NAME].
Description
2 or more ST_COMMENT feature with same value of tagset_id qualifiers are found in an entry.

JP0160
Format
JP0160:ER1:STX:ANN:Lines [#N1] and [#N2]: 2 or more [ tagset_id ] qualifiers are found in [ ST_COMMENT ] feature.
Description
The tagset_id qualifier can be specified only one for the ST_COMMENT feature. Please delete one of them.

JP0161
Format
JP0161:WAR:STX:ANN:Lines [#N1] and [#N2]: 2 or more [#QUALIFIER NAME] qualifiers are found in [ ST_COMMENT ] feature.
Description
2 or more qualifiers are found in the ST_COMMENT feature. Please delete one of them, if necessary.

JP0162
Format
JP0162:ER1:STX:ANN:Line [#N]: [#QUALIFIER NAME] qualifier is found in [ COMMON ] entry.
Description
Invalid qualifier is entered in COMMON entry. Please correct it.

JP0163
Format
JP0163:ER2:STX:ANN:Line [#N]: To use [#QUALIFIER NAME1] qualifier [#VALUE], [#QUALIFIER NAME2] qualifier is required in the [#FEATURE NAME] feature.
Description
When the value of exception qualifier is "annotated by transcript or proteomic data", inference qualifier is required in the CDS feature.

JP0164
Format
JP0164:WAR:STX:ANN:Line [#N]: The [ artificial_location ] qualifier is used.
Description
The use of artificial_location qualifier is allowed only for genome-scale annotation.

JP0165
Format
JP0165:WAR:STX:ANN:Line [#N]: When an entry has [ mRNA ] or [ operon ] feature, [ mol_type ] should be [ genomic DNA ].
Description
Since mRNA or operon feature should be described as a genome annotation, please confirm the mol_type.

JP0166
Format
JP0166:ER2:STX:ANN:Line [#N]: [#QUALIFIER NAME] qualifier is not recommended for [#FEATURE NAME] feature.
Description
The combination of feature and qualifier is not recommended for new submissions.
Please correct according to Feature/Qualifier Usage Matrix.
If you need to describe it, please contact us.

JP0167
Format
JP0167:ER2:STX:ANN:Line [#N]: [#FEATURE NAME] feature is not recommended.
Description
The feature is not recommended for new submissions.
If you need to describe it, please contact us.

JP0168
Format
JP0168:WAR:LOC:AxS:Line [#N]: Locations of [ PRIMARY_CONTIG ] features are not covered full length of entry.
Description
The sequence length is greater than all location ranges of PRIMARY_CONTIG features.
Please check alignment between its sequence and cited sequences and locations of PRIMARY_CONTIG features, and correct them, if necessary.

JP0169
Format
JP0169:WAR:STX:ANN:Line [#N]: [#COUNTRY NAME] is old country name. See [ http://www.ddbj.nig.ac.jp/sub/ref6-e.html#country ].
Description
You described an old country name for value of country qualifier.
Please update it to the current name, when feasible.

JP0170
Format
JP0170:ER1:STX:ANN:Line [#N]: To use [#QUALIFIER NAME1] qualifier, [#QUALIFIER NAME2] or [#QUALIFIER NAME3] qualifier is required in the [#FEATURE NAME] feature.
Description
When you use qualifier 1, qualifier 2 or qualifier 3 is required for the feature.

JP0171
Format
JP0171:WAR:STX:ANN:Line[#N]: Different set [#QUALIFIER NAME1] and [#QUALIFIER NAME2] found in [#FEATURE LINE].
Description
The pair, qualifier 1 and qualifier 2, are found in other feature(s), however, the values are not described in the same way among the features.
Please correct them, if necessary.

JP0172
Format
JP0172:ER1:STX:ANN:Line [#N]: To use [#QUALIFIER NAME1] qualifier [#VALUE], [#QUALIFIER NAME2] qualifier is required in the [#FEATURE NAME] feature.
Description
When the value of gap_type qualifier is "within scaffold" or "repeat within scaffold", linkage_evidence qualifier is required for the assembly_gap feature.

JP0173
Format
JP0173:ER2:STX:ANN:Line [#N]: The [ pseudo ] qualifier is used.
Description
The pseudo qualifier is used. , Please replace it by pseudogene qualifier, if necessary.

JP0174
Format
JP0174:WAR:LOC:ANN:Line [#N]: The location of [ source ] feature is partial.
Description
The partial flag, "<" and/or ">", is found in the location of source feature. Please remove it.

JP0175
Format
JP0175:ER1:LOC:ANN:Line [#N]: Partial flag is found in the mid of location.
Description
The partial flag, "<" and/or ">", is found in the mid of location. Please correct it according to Description of Location.

JP0176
Format
JP0176:WAR:LOC:ANN:Lines [#N1] and [#N2]: [#ENTRY NAME]: [ gap or assembly_gap ] feature [#LOCATION VALUE1] is overlapped with [ CDS ] feature [#LOCATION VALUE2].
Description
There is some region in the location of either of gap or assembly_gap features overlapping with a CDS feature.
Please divide CDS into two CDS features to avoid the overlap, if necessary.

JP0177
Format
JP0177:WAR:STX:ANN:Line [#N]: [#VALUE] in [#QUALIFIER NAME] qualifier is not defined in standard list.
Description
The value for tagset_id qualifier in ST_COMMENT feature is not included in the standard list.
Please reconfirm it, and, if necessary, correct it.

JP0178
Format
JP0178:WAR:STX:ANN:Line [#N]: [#QUALIFIER NAME] in [#FEATURE NAME] feature is not defined in standard list.
Description
The qualifier name in ST_COMMENT feature is not included in the standard list.
Please reconfirm it, and, if necessary, correct it.

JP0179
Format
JP0179:WAR:LOC:ANN:Line [#N]: [#ENTRY NAME]: The location [#LOCATION VALUE] of [#FEATURE NAME] feature is longer than [#LOCACTION_LIMIT].
Description
The length of unsure feature location is greater than 10.
Please reconfirm it, and, if necessary, correct it.

JP0180
Format
JP0180:ER1:STX:ANN:Line [#N]: To use [#QUALIFIER NAME1] qualifier [#VALUE], [#QUALIFIER NAME2] qualifier can NOT be used in the [#FEATURE NAME] feature.
Description
In assembly_gap feature, the value of gap_type qualifier is not appropriate, or the linkage_evidence qualifier should be removed.
Please confirm and correct it.

JP1015
Format
JP1015:ER2:STX:ANN: [ DATATYPE/type ] [#TYPE VALUE] is not specified at [ COMMON ] entry, though the specific keyword [#KEYWORD VALUE] is found.
Description
The given keyword is specific to some DATATYPE, however, the DATATYPE/type is not specified in the COMMON entry.

JP1027
Format
JP1027:ER1:STX:ANN: MGA:[#FEATURE NAME] feature is required for [ COMMON ] entry.
Description
For MGA, all of features, SUBMITTER, REFERENCE and source, are required for COMMON entry.

JP1028
Format
JP1028:ER1:STX:SEQ:Line [#N]: MGA:[#FIELED NAME] is including invalid character(s).
Description
For MGA, the header line for the sequence includes some invalid character(s). Please revise it.

JP1029
Format
JP1029:ER1:STX:ANN:Line [#N]: TPA:[ status/Published Only in Database ] can NOT be selected in [ REFERENCE ] feature, [#ENTRY NAME].
Description
In TPA submission, "Published Only in Database" cannot be specified for the status qualifier in the REFERENCE feature.

JP1030
Format
JP1030:ER1:STX:ANN:Line [#N]: [ PRIMARY_CONTIG ] feature is found, though [ DATATYPE/type=TPA ] or [DIVISION/division=TSA ] is not specified at [ COMMON ] entry.
Description
Neither DATATYPE/type=TPA nor DIVISION/division=TSA is specified in COMMON entry, though the PRIMARY_CONTIG feature that is specific to TPA or TSA entry is used.

JP1032
Format
JP1032:ER1:LOC:ANN:Line [#N]: [#LOCATION VALUE]: Invalid position is specified at start or end.
Description
The combination of the start and the end positions is invalid in the description of the location.
The direction of the location can be only described from 5' to 3'.
i.e. "500..345" --> "complement(345..500)"

JP1033
Format
JP1033:ER1:LOC:ANN:Line [#N]: [#LOCATIONE_OPEREATOR] is invalid.
Description
There is only one piece of "join" or "order" in the description of the location. Please correct it.
i.e. "join(1..100)" → "1..100"

JP1034
Format
JP1034:ER1:LOC:AxS:Line [#N] in annotation file: [#LOCATION VALUE] is out of sequence range of the entry [#ENTRY NAME].
Description
The specified location in the annotation file is greater than the sequence length in the sequence file.

JP1036
Format
JP1036:ER1:STX:ANN:Line [#N]: Both [#QUALIFIER NAME1] and [#QUALIFIER NAME2] qualifiers are found.
Description
Please remove either one of two qualifiers, because both of two cannot be used in the same feature.

JP1038
Format
JP1038:ER1:STX:ANN:Line [#N]: No qualifier is found before specified value column.
Description
Though the value is described, no corresponding qualifier is found in the line.
Please specify some appropriate qualifier.

JP1039
Format
JP1039:ER1:STX:ANN:Lines [#N1] and [#N2]: [#FEATURE NAME] feature has the same information.
Description
The same features whose locations and qualifiers cannot be distinguished are found at 2 lines.
Please confirm and correct them.

JP1042
Format
JP1042:ER1:STX:ANN:Line [#N1]: The value [#VALUE] for [ citation ] is greater than the number of REFERENCEs, [#N2].
Description
The value of the citation qualifier is greater than the number of REFERENCE features.

JP1044
Format
JP1044:ER1:SYS: Work is stopped because [#FILE NAME] is not found.
Description
The checking process is stopped, because the file cannot be opened.

JP1045
Format
JP1045:ER2:STX:ANN:Line [#N]: [#QUALIFIER NAME] is NOT found in [ source ] feature, though it is referred by [ ff_definition ].
Description
The qualifier specified by the meta-description in the "ff_definition" is not found in the source feature.

JP1046
Format
JP1046:ER2:STX:ANN:Line [#N]: 2 or more [#QUALIFIER NAME] are found in [ source ] feature, though it is referred by [ ff_definition ].
Description
The qualifier specified by the meta-description in the "ff_definition" is found two or more times in the source feature.

JP1048
Format
JP1048:ER1:STX:ANN:Entry [#ENTRY NAME]: TPA entry must have [#FEATURE NAME] feature.
Description
Specified feature required for TPA submission is not found.

 

List of transChecker error messages

In this section, brief explanations for all transChecker error messages are listed.
See also Format of transChecker error messages.
When some error messages are found, it is required to be resolved them by modification of files, in principle.
If you have any problems and/or questions, please contact us with error messages.

Terms and numbers closed with brackets ( [ and ] ) and started from #, are substituted by each real value that is used in your submission.

Terms closed with brackets ( [ and ] ) and not started from # are the reserved words for features or qualifiers.

You can search explanations for transChecker error messages by selecting from the following box;


TC0004
Format
TC0004:FAT: Unable to execute transChecker.
Description
This tool can not be started.
Since it is probably caused by system disorder, please contact us.

TC0005
Format
TC0005:ER2: Description of location [#LOCATION VALUE] is illegal.
Description
The location of CDS feature is invalid. It is required to fix the error.
Please refer to Description of Location to correct it.

TC0006
Format
TC0006:ER2: Amino acid [#ABBREVIATION] in [transl_except] qualifier is illegal.
Description
The error related to transl_except qualifier.
When you find it, correction is required.
The three-letter abbreviation of amino acid in the value of transl_except qualifier is invalid.
Please confirm the acceptable abbreviations in the site; Amino Acid Codes.

TC0007
Format
TC0007:ER2: Value of [#QUALIFIER NAME] qualifier [#VALUE] is invalid.
Description
The error related to codon_start, transl_except, or transl_table qualifier.
When you find it, correction is required.
Please refer to the format of the qualifier to correct it.

TC0008
Format
TC0008:ER2: Base range of [transl_except] qualifier [#VALUE] is overlapped.
Description
The error related to transl_except qualifier.
When you find it, correction is required.
Some locations (<base_range>) in values of transl_except qualifiers are overlapped each other.
So, amino acid translation is performed with regardless transl_except qualifiers.

TC0009
Format
TC0009:ER2: Base range of [transl_except] qualifier [#VALUE] is invalid.
Description
The error related to transl_except qualifier.
When you find it, correction is required.
The location (<base_range>) in value of transl_except qualifier is invalid.
Please refer to the format of transl_except qualifier to correct it.

TC0011
Format
TC0011:ER2: [#QUALIFIER NAME] qualifier is duplicated. The value is automatically set 1.
Description
The error related to codon_start or transl_table qualifier.
When you find it, correction is required.
Amino acid translation is performed as the default value, "1".
There are two or more qualifiers in a CDS feature, though the qualifier is available only one by one CDS feature.
Amino acid translation is performed as the default value, "1".

TC0015
Format
TC0015:ER2: Entry [#ENTRY NAME] is NOT found in sequence file.
Description
The entry name specified in the annotation file is not found in the sequence file.
Confirm and correct the entry name.

TC0016
Format
TC0016:ER2: Untranslatable codon [#CODON] is found in the sequence range.
Description
In the sequence file, an invalid code is found. Confirm and correct the sequence file.
See the acceptable nucleotide codes.

TC0017
Format
TC0017:ER2: First codon [#CODON] is not a start codon.
Description
The CDS feature is not started by initiation codon. Confirm and correct it.
If the CDS feature is not complete at 5' end, use partial symbol "<" in the location.

TC0018
Format
TC0018:ER2: Final codon [#CODON] is not a stop codon.
Description
The CDS feature is not ended by termination codon. Confirm and correct it.
If the CDS feature is not complete at 3' end, use partial symbol ">" in the location.

TC0019
Format
TC0019:ER2: Stop codon is found in mid of CDS location.
Description
Termination codon is found in the mid of the location of the CDS feature. Confirm and correct it.

TC0020
Format
TC0020:WAR: [#QUALIFIER NAME] qualifier should be selected. The value is automatically set 1.
Description
Either of codon_start or transl_table qualifier is unspecified.
Amino acid translation is performed as the default value, "1".

TC0022
Format
TC0022:ER2: Base range of [transl_except] qualifier [#VALUE] is mismatched in reading frame.
Description
The error related to transl_except qualifier.
When you find it, correction is required.
Since the base range of transl_except qualifier is not matched in reading frame of CDS feature, correct the <base_range> of transl_except qualifier.

TC0023
Format
TC0023:ER2: Amino acid of [transl_except] qualifier [#VALUE] is not changed from conceptual translation.
Description
The error related to transl_except qualifier.
When you find it, correction is required.
Since the amino acid of transl_except qualifier is identical to conceptual translation of CDS feature, remove the transl_except qualifier.

TC0024
Format
TC0024:WAR: Amino acid of [transl_except] qualifier [#VALUE] is not [Met].
Description
Since you do not specify the amino acid, Met, with the transl_except qualifier, translation start site is not "M".

TC0025
Format
TC0025:ER2: Amino acid of [transl_except] qualifier [#VALUE] is not [TERM].
Description
The error related to transl_except qualifier.
When you find it, correction is required.
Since you do not specify stop codon with transl_except qualifier, the end of CDS location is not stop codon.
Correct CDS location or the value of transl_except qualifier.

TC0026
Format
TC0026:ER2: Stop codon is specified by [transl_except] qualifier [#VALUE] in mid of CDS location.
Description
The error related to transl_except qualifier.
When you find it, correction is required.
Since you specify stop codon with the transl_except qualifier, a stop codon is found in the mid of CDS feature.
Remove the transl_except qualifier.

TC0029
Format
TC0029:WAR: [#N] codons are not translatable.
Description
During amino acid translation of CDS feature, N of codons can not be translated into any of specific amino acids.

TC0030
Format
TC0030:FAT: Proper [#FILE NAME] is not found in [#FOLDER NAME] folder.
Description
The resource file required to run transChecker is not in the directory.

 

List of AGPParser error messages

In this section, brief explanations for all AGPParser error messages are listed in the code number order.
See Format of AGPParser error messages.
When some error messages are found, it is required to be resolved them by modification of files, in principle.
If you have any problems and/or questions, please contact us with error messages.

Terms and numbers closed with brackets ( [ and ] ) and started from #, are substituted by each real value that is used in your submission.

You can search explanations for AGPParser error messages by selecting error code from the following box;


AP0001
Format
AP0001:FAT: System error [#MESSAGE].
Description
Unforeseen error is found. Please contact us.

AP0002
Format
AP0002:FAT: [#FILE NAME] cannot be opened.
Description
Some error is found during opening the specified file.

AP0005
Format
AP0005:ER1: Line [#N]: Invalid AGP format. Number of columns must be 9.
Description
The number of columns in a line must be 9, however, the line is not 9 in its number of columns.

AP0006
Format
AP0006:ER1: Line [#N]: Invalid AGP format. Illegal value [#VALUE] at column [#COLUMN_NAME].
Description
The value of the column in the line is invalid.

AP0007
Format
AP0007:ER2: Line [#N]: Inconsistency between [#COLUMN_NAME1] and [#COLUMN_NAME2].
Description
Some inconsistency is found in the values between gap_type and linkage or linkage and linkage_evidence.

AP0009
Format
AP0009:ER2: Object [#OBJECT]: Minimum value of object_beg [#OBJECT_BEG] is not [1].
Description
In an object, the minimum value of object_beg must be "1", however, it is not "1".

AP0010
Format
AP0010:ER2: Object [#OBJECT]: Maximum value of object_end [#OBJECT_END] is not same to sum of component lengths.
Description
In the object, the maximum value of object_end must be sum of all component lengths.

AP0012
Format
AP0012:ER2: Line [#N]: Range of object is different from span of component.
Description
The range between object_beg and object_end is different from the range between component_beg and component_end.

AP0013
Format
AP0013:ER2: Line [#N]: Range of object is different from gap_length.
Description
The range between object_beg and object_end is different from the value of gap_length.

AP0014
Format
AP0014:ER2: Line [#N]: Length of unknown gap must be [100].
Description
The gap that cannot be estimated its length must be set 100.

AP0015
Format
AP0015:WAR: [#COMPONENT_ID] is not found in [#RESOURCE].
Description
The cited sequence specified as this component_id is not found in the file.

AP0016
Format
AP0016:ER2: [#COMPONENT_ID] is not found anywhere.
Description
The component is not found.

AP0017
Format
AP0017:ER2: Line [#N]: [#COMPONENT_ID]:[#COMPONENT_BEG]..[#COMPONENT_END] is duplicated in the object [#OBJECT].
Description
The region of the component is cited two or more times in the object.

AP0018
Format
AP0018:ER2: Line [#N]: [#COMPONENT_ID]:[#COMPONENT_BEG]..[#COMPONENT_END] is out of range for its sequence.
Description
The specified region of the component is out of cited sequence range in the multi-fasta file.

AP0021
Format
AP0021:ER1: [#FILE NAME] is not found.
Description
The specified file is not found.

AP0027
Format
AP0027:WAR: Line [#N]: [#COMPONENT_ID] is not in accession.version format at [ component_id ] column.
Description
When you cite an accession number as a component_id, its version number is required.

AP0029
Format
AP0029:ER1: Line [#N]: [#COMPONENT_ID] has invalid version at [ component_id ] column (0 < version).
Description
When you cite an accession number as a component_id, its version number must be a positive integer.