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.

Parser error mesages

General notice
1) The output of error message is in the following format;
[Code Number]:[Level]:[Type]:[File]:[Region]:[Body Text]

Code Number; Indicate the code number of the message
Level; Indicate the level of the message;: ER1; Type 1 error of the file format. Correction is required.
ER2; Type 2 error of the file format. Correction is required.
FAT; Fatal error, related to system environment.
WAR; Warning for the file format. Correction is sometimes required.
MES; Reference message for some other error(s).
Type; Indicate the category of the message;: STX; Syntax
SYS; Related to the checking performance
LOC; Compare between sequence and location
File; Indicate the file occurred the problem;: ANN; Annotation file
SEQ; Sequence file
AxS; comparison between Annotation and Sequence files
Region; Indicate the region of the error as line number and/or entry name
Body Text; Detail descriptions of the message

2) Terms and numbers closed with brackets ([ and ]) and started from "#", are substituted by each real value that is used in your annotation or sequence files.

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

The explanations for all error messages are shown in code number order.

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 gap or assembly_gap feature is invalid.
The direction of the gap location can be only described from 5' to 3'.
Any operators, "join", "order" or "complement" are not acceptable for the location of gap or assembly_gap feature.

JP0048

Format: JP0048:ER1:STX:ANN:Line [#N]: [#ENTRY NAME]: the span length of [#FEATURE NAME] [#LOCATION VALUE] location is not 100 bp, though it has unknown [ estimated_length ] qualifier.
Description: The length of gap or assembly_gap location is not 100 bp.
Please revise it to be 100 bp.
Because it is required to be 100 bp when the estimated_length of the gap region is unknown.

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].
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 ] the specific keyword [#KEYWORD VALUE] is found.
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].
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].
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.

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.
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.

transChecker error messages

The "transChecker" is a tool for checking amino acid sequences translated from CDS features.
When some errors are found, it is required to correct and to fix them before your submission.

Format of error messages
If there is no error, this tool does not dump any error messages.

Format
>[Entry name].[Serial number of CDS feature][Space][Location of CDS feature]
Error message 1
Error message 2
:
:
Error message N
//

Each error message is described in the format, " [Level] <message body> ".
The header, [Level] shows error type. There are three error types, [FATAL], [ERROR], and [WARNING].
The main part, <message body> shows each detected error in detail.

For example
>entry1.1 <1..>366
[WARNING] 'codon_start' qualifier should be selected. The value is automatically set 1.
[WARNING] 'transl_table' qualifier should be selected. The value is automatically set 1.
//
>entry2.3 4315..4997
[ERROR] First codon [cct] is not a start codon.
[ERROR] Final codon [cat] is not a stop codon.
[ERROR] Stop codon '*' is found in the range.
//

Format of amino acid sequence file
The amino acid sequence file is a kind of fasta format.

When some errors are occurred, the sequence of CDS feature is translated into amino acid as is, however, some translation processes are likely skipped because of severe errors.

Format
>[Entry name].[Serial number of CDS feature][Space][Location of CDS feature]
Amino acid sequences (60 letters/line)
//

For example
>entry1.1 89..406
MLARISELTKIGTTIFIVAIDQVAEPNSWGSSQLVLLAKIAGALKAIPPNPVCTSRHRQA
ASVSPFRSAIVGTLLQLEAIKNLLTVSVDTIQQNGVLFIFVALLR
//
>entry1.2 684..1325
MSIGILGTKLGMTQIFDESGKAVPVTVIQAGPCPITQIKTVATDGYNAIQIGFLEVREKQ
LSKPELGHLSKAGAPPLRHLLEYRVPSTDGLELGQALTADRFEAGQKVDVQGHTIGRGFT
GYQKRHGFARGPMSHGSKNHRLPGSTGAGTTPGRVYPGKRMAGRSGNDKTTIRGLTVVRV
DADRNLLLVKGSVPGKPGALLNITPATVVGQQA
//

Error messages

In this section, brief explanations for error messages are listed in their levels.
When some error messages are found, it is required to correct and to fix them.
If you have any problem and/or questions, please contact us with error messages.

ERROR level

The ERROR level messages mean that transChecker finds some mistakes in annotation or sequence file.
If some of the following ERROR level messages are found, it is required to correct and to fix it.
Red term(s) closed with brackets ([ and ]) and started from "#", are substituted by each real value
that is used in the checked files, "annotation file" or "sequence file".
4-2-1. Location
The error is related to the location of CDS feature. When you find the message, correction is required.

Format: [ERROR] Description of Location [#location of CDS feature] is illegal.
Description: The location of CDS feature is invalid. Please refer to Description of Location to correct it.

Format: [ERROR] 'codon_start' qualifier is duplicated. The value is automatically set 1.
Description: The error related to codon_start qualifier.
When you find some of follows, correction is required.
There are two or more codon_start qualifiers in the CDS feature, though the qualifier is available only one by one CDS feature.
Amino acid translation is performed as default value, "1".

Format: [ERROR] 'codon_start' qualifier has invalid value [#Value].
Description: The error related to codon_start qualifier.
When you find it, correction is required.
The value of codon_start qualifier is invalid. Either of "1", "2" or "3" is acceptable.

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

Format: [ERROR] 'transl_table' qualifier has invalid value [#Value].
Description: The error related to transl_table qualifier.
When you find it, correction is required.
The value of transl_table qualifier is invalid.
You can see all of available codon tables in The Genetic Codes

Format: [ERROR] Amino acid abbreviation [#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.

Format: [ERROR] 'transl_except' qualifier has invalid value [#Value].
Description: The error related to transl_except qualifier.
When you find it, correction is required.
The value of transl_except qualifier is invalid.
Please refer to the format of transl_except qualifier to correct it.

Format: [ERROR] Location 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.

Format: [ERROR] Location 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.

Format: [ERROR] 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.

Format: [ERROR] 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.

Format: [ERROR] 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.

Format: [ERROR] 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.

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

Format: [ERROR] Untranslatable codon [#Codon] is found in the sequence range.
Description: Since untranslatable codon is found in the nucleotide sequence, amino acid translation is failed.

Format: [ERROR] 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.

Format: [ERROR] 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.

Format: [ERROR] Stop codon '*' is found in the range.
Description: Termination codon is found in the mid of the location of the CDS feature. Confirm and correct it.

WARNING level

The WARNING level messages mean that transChecker calls for attentions.
If some of the following messages are found, please confirm and fix it, if necessary.

Format: [WARNING] 'codon_start' qualifier should be selected. The value is automatically set 1.
Description: The codon_start qualifier is not specified.
Amino acid translation is performed as the default value, "1".

Format: [WARNING] 'transl_table' qualifier should be selected. The value is automatically set 1.
Description: The transl_table qualifier is not specified.
Amino acid translation is performed as the default value, "1".

Format: [WARNING] Amino acid of 'transl_table' 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".

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

FATAL level

The error messages in FATAL level mean some disorders of transChecker (absence of resource file, etc.) are probably found.

Format: [FATAL] Proper 'codon.table' is not found in 'resource/codon' folder.
Description: The resource file, codon.table, is not in the directory, resource/codon.

Format: [FATAL] Proper 'amino.table' is not found in 'resource/codon' folder.
Description: The resource file, amino.table, is not in the directory, resource/codon.

Format: [FATAL] Proper 'transltabs.list' is not found in 'resource/FQ' folder.
Description: The resource file, transltabs.list, is not in the directory, resource/FQ.

Format: [FATAL] Unable to execute Translation.
Description: This tool can not be started. Since it is probably caused by system disorder, please mail to us with error messages.

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