| Severity |
Error Code |
Description |
Rule |
| Error |
E0001_FileNotFound |
The input file ({{ file_name }}) is not found. |
|
| Error |
E0002_File_Not_Readable |
Unable to open the input file {{ ds_file_name }}. |
|
| Error |
E0003_File_Empty |
File was found empty |
|
| Warning |
E0004_Unsupported_File_Extensions_Detected |
The uploaded file extension is not automatically processed and will require manual intervention. |
The supported file extensions for automated processing are: txt, csv, dat, xlsx |
| Warning |
E0005_Multiple Phenotype Files Detected |
Multiple Pheno files are detected. The uploaded files are not automatically processed and will require manual intervention. |
Processing of multiple submitted PHENO files require manual intervention |
| Error |
E0006_Incomplete_Plink_Set |
Description: PLINK set incomplete. All PLINK file submissions MUST include a complete set of .bim, .fam and .bed files. |
PLINK sets are processed as a triplet of files .bim, .fam and .bed. |
| Error |
E0101_Blank_Id_Value |
Missing IDs are not allowed in primary subject ID and sample ID columns. Add missing IDs into column or remove the row. |
Empty value is not allowed in the Subject ID and Sample ID columns. |
| Error |
E0102_Duplicated_Id |
IDs are duplicated. Each person should only have a single subject ID; each sample ID should be represented in a single row. Remove repeating IDs. |
Duplicate values are not allowed in the Sample ID or in the Subject ID columns of the DS files (except for longitudinal datasets). For parent SSM, the sample ID should be unique within each substudies. |
| Error |
E0103_Invalid_Id_Value |
Remove invalid characters. Only the following characters can be included in the ID: English letters, Arabic numerals, period (.), hyphen (-), underscore (_), at symbol (@), and the pound sign (#). |
The characters other than a-z, A-Z, 0-9, ., -, @, and # are not allowed in the Subject_ID and Sample_ID columns. |
| Error |
E0104_Invalid_Consent_Value |
The CONSENT column can only have integer values '>=0'. |
Invalid consent values: If the Consent column is numerical, then the Consent column is allowed to have only integer values. |
| Error |
E0105_StudyDirectoryNotFound |
Study directory not found. |
Error finding directory |
| Error |
E0106_MissingSubjectConsentFile |
Subject Consent file is missing. |
Error finding Subject Consent file |
| Error |
E0107_MissingSubjectSampleMappingFile |
Subject Sample Mapping file is missing. |
Error finding Subject Sample Mapping file |
| Error |
E0108_MissingMetaDataFile |
Metadata file is missing. |
Error finding Metadata file |
| Error |
E0109_Subject_IDs_Mismatch_SSM2SC |
The SSM subject IDs are not found in the Subject Consent DS. Therefore, the subjects in the SSM DS are not consented. Either remove the row with the unconsented subject from the SSM DS or add the unconsented subject to the Subject Consent DS with valid consent. |
SSM ids are not a subset of subject consent ids. |
| Error |
E0110_Column_Name_Mismatch_SSM2SC |
The Subject ID variable names are different in the Subject Consent and SSM files. They must be the same. |
SC subject id column and SSM subject id column must match. |
| Error |
E0111_Multiple_NonBlank_Sheets |
Excel file has multiple sheets. Fix by submitting one sheet per file. |
The excel file should have only single worksheet in DD or DS file. |
| Error |
E0112_Incorrect_FileType_Detected_DS |
File is marked as a Dataset (DS), but does not look like a DS; there are no ID columns. |
Dataset file is expected to have correct file type. |
| Error |
E0113_Incorrect_FileType_Detected_DD |
File is marked as a Data Dictionary (DD), but does not look like a DD; there is no VARNAME. |
Data Dictionary file is expected to have correct file type. |
| Error |
E0114_Duplicate_Variable_Names |
Variable names must be unique. Change one of the variable names or remove the entire variable if redundant. |
Variable names should be unique in data dictionary file. |
| Error |
E0116_Duplicate_Rows_In_DD |
Duplicate rows found in data dictionary file. Each row in data dictionary should be unique. Remove duplicates and replace file. |
Duplicate rows not allowed in data dictionary file. |
| Error |
E0117_Duplicate_Rows_In_DS |
Duplicate rows found in dataset file. Each row in dataset should be unique. Remove duplicates and replace file. |
Duplicate rows not allowed in dataset file. |
| Error |
E0118_Missing_VARDESC_Column |
Data dictionary file missing required VARDESC column. |
VARDESC column is required in data dictionary file. |
| Error |
E0119_Blank_VARDESC |
All variables must have a value for VARDESC. |
VARDESC column value cannot be blank in data dictionary file. |
| Error |
E0120_Blank_VARNAME |
All variables must have a value for VARNAME. |
VARNAME column value cannot be blank in data dictionary file. |
| Error |
E0121_Non_ASCII_Characters |
Remove non ascii characters from dataset and data dictionary files. |
Non ASCII Characters not allowed in dataset and data dictionary file. |
| Warning |
E0122_Unique_Keys_Detected |
More than one unique key detected. |
Found more than one unique keys in data dictionary file. |
| Error |
E0123_Unmatched_Variables_In_DS |
All variables in DS must be found in DD. Either 1) Add variable in DD or 2) Remove the variable column in DS. |
Found unmatched variables in dataset file. |
| Warning |
E0124_Unmatched_Variables_In_DD |
DD has variables not found in DS. Add variables in DS, if needed. |
Found unmatched variables in data dictionary file. |
| Error |
E0125_Subject_ID_Mismatch |
Unconsented subjects or subjects with CONSENT=0 have been found in the Subject Phenotypes DS. Either 1) remove the subject IDs with invalid consent from the Subject Phenotypes DS or 2) add the subject IDs to the Subject Consent DS with valid consent. |
Subject IDs found in Subject Phenotype dataset file must be found in Subject Consent dataset file. |
| Error |
E0126_Sample_ID_Mismatch |
Sample IDs belonging to unconsented subjects or subjects with CONSENT=0 have been found in the Sample Attributes DS. Either 1) remove the sample IDs belonging to subjects with invalid consents or 2) add the sample ID to the Subject Sample Mapping (SSM) DS by mapping to a subject ID with valid consent. |
Sample IDs found in Sample Attribute dataset file must be found in Subject Sample Mapping dataset file. |
| Error |
E0127_Blank_Row |
Blank row detected in DD. Remove blank rows. |
Blank rows not allowed in middle of data in data dictionary files. |
| Error |
E0128_Invalid_Characters |
VARNAME column values were found with invalid characters. |
Invalid characters like '' or 'dbGaP' not allowed in data dictionary files. |
| Error |
E0129_Non_Unicode_Characters |
Non Unicode characters not allowed in data dictionary file. |
Non unicode characters not allowed in data dictionary files. |
| Error |
E0130_MissingSubjectSampleMappingDataDictionaryFile |
Subject Sample Mapping Data Dictionary file is missing. |
Error finding Subject Sample Mapping Data Dictionary file |
| Error |
E0131_MissingSubjectPhenotypeDataDictionaryFile |
Subject Phenotype Data Dictionary file is missing. |
Error finding Subject Phenotype Data Dictionary file |
| Error |
E0132_MissingSubjectPhenotypeDatasetFile |
Subject Phenotype Dataset file is missing. |
Error finding Subject Phenotype Dataset file |
| Error |
E0133_MissingSampleAttributeDatasetFile |
Sample Attribute Dataset file is missing. |
Error finding Sample Attribute Dataset file |
| Error |
E0134_MissingSampleAttributeDataDictionaryFile |
Sample Attribute Data Dictionary file is missing. |
Error finding Sample Attribute Data Dictionary file |
| Error |
E0135_MissingPedigreeDataDictionaryFile |
Pedigree Data Dictionary file is missing. |
Error finding Pedigree Data Dictionary file |
| Error |
E0136_Consent_Missing_In_SC_DS |
Consent code is found in the Subject Consent DD, but not used in the Subject Consent DS. Remove unused code from the DD OR add subjects with the missing code in the DS. All consents being used should be registered in the dbGaP Submission System. |
The consent codes listed in Subject Consent DS must match the consents codes in the values columns of Subject Consent DD. |
| Error |
E0137_Consent_Missing_In_SC_DD |
Consent code is found in the Subject Consent DS, but is not coded in the Subject Consent DD. Add the missing consent codes and values to the DD OR remove the unconsented subjects OR change the consent in the DS to a valid value. All consents being used should be registered in the dbGaP Submission System. |
The consent codes listed in Subject Consent DS must match the consents codes in the VALUES columns of Subject Consent DD. |
| Error |
E0138_Consent_Mismatch_SC_DD_vs_RS |
Consents in the DD do not match the consents registered in the dbGaP Submission System (SS). Correct the DD or contact your GPA if the consents in the SS need to be updated. IMPORTANT: If the consent is not registered as you expect, please contact your Genomic Program Administrator (GPA) to change the consent. GPA:{{ gpa_email_list }} |
The consents listed in Subject Consent DD must match the consents registered for the study. |
| Error |
E0139_Duplicated_ID_In_Subject_Consent |
IDs are duplicated. Each person should only have a single subject ID represented in a single row. Remove repeating IDs. |
Duplicate values are not allowed in the Subject ID column of the Subject Consent DS file. |
| Error |
E0202_Sample_Id_Mismatch_Geno2SSM |
Sample IDs in genotype dataset are not found in the SSM DS. These samples do not belong to consented subjects. Either 1) add sample IDs to the SSM DS and Sample Attributes DS or 2) remove sample IDs from genotype dataset. |
Sample IDs are used in the genotype file |
| Error |
E0203_Subject_Id_Used_In_Geno_Files |
The IDs in genotype dataset match the subject IDs and not sample IDs in the SSM DS. If subject ID and sample ID are same, repeat the subject ID in the sample ID column of the SSM DS. |
Subject IDs are used in the genotype file |
| Error |
E0208_MissingSubjectConsentDataDictionaryFile |
Subject Consent Data Dictionary file is missing. |
Error finding Subject Consent Data Dictionary file |
| Error |
E0521_Pedigree_Parent_Cross_Subject |
Parent(s) from the Pedigree file are missing from the Subject Consent |
Pedigree's parent must be listed in the Subject Consent |
| Error |
E0506_Pedigree_Subject_Duplicates |
Pedigree subject IDs are duplicated. Remove duplicated subject IDs so that each subject ID appears once. |
Values in SUBJECT_ID column are unique. |
| Error |
E0507_Pedigree_Parent_Not_Subject |
Father or mother IDs are not found in the subject ID column. Add missing father or mother IDs in the subject ID column of the Pedigree DS and include family ID and sex on the same row. Also, verify that the father and mother IDs are also included in the subject ID column of the Subject Consent DS with consent > 0 if consented or consent = 0 if parent is a linking member and not consented. |
All values in FATHER and MOTHER columns should be listed in SUBJECT_ID column. |
| Error |
E0508_Pedigree_Columns_Count |
Missing required column(s). The required columns in the Pedigree DS are family ID, subject ID, father, mother, and sex. MZ twin IDis required if there are monozygotic twins. |
Include the columns family ID, subject ID, father, mother, sex, and the optional MZ_TWIN_ID only if the file contains monozygotic twins. |
| Error |
E0509_Pedigree_Nulls |
Family IDs or subject IDs are missing. IDs are required. |
Columns 1 and 2 should not have null values. Other columns may. |
| Error |
E0510_Rectangular_File |
Dataset is not rectangular. Remove extra values. |
The numbers of cells on each row of the file should match the number of column headers in the file. |
| Error |
E0511_Ped_SC_Subject_Value |
Subject IDs in Pedigree file DS do not exist in Subject Consent DS. Add the subject ID to Subject Consent DS with valid consent value. Use consent 0 if this subject is for linking subjects in the pedigree. |
All values in <SUBJECT ID> column of Pedigree File should be listed in <SUBJECT_ID> column of Subject Consent File |
| Error |
E0512_Ped_SC_SubjectColumn_Name |
The Pedigree subject ID variable name in the Pedigree files do not match the Subject Consent files. Use the same variable name for subject IDs throughout all the datasets. |
The header name of <SUBJECT ID> column of Pedigree File should match header name to <SUBJECT_ID> column of Subject Consent File. |
| Error |
E0513_Pedigree_Twin_Values |
MZ twin IDs are listed once. Add the same MZ twin ID for the related twin or remove the single MZ twin ID. |
Monozygotic twins and multiples should be assigned the same MZ_TWIN_ID but different SUBJECT_IDs. For dizygotic twins and all other individuals, this column should be left blank. |
| Error |
E0514_Pedigree_Twin_Parents |
Twins are listed with different parents. Change the parent IDs so that they are the same for MZ twins or remove the MZ twin ID designation. |
Monozygotic twins and multiples should be assigned the same MZ_TWIN_ID but different SUBJECT_IDs and have the same Mother and Father. Please correct and resubmit file. |
| Error |
E0515_Pedigree_Twin_Sex |
MZ twins are listed with different sex values. Change the sex value for one of the twins or remove the MZ twin ID designation. |
Monozygotic twins and multiples should be assigned the same MZ_TWIN_ID but different SUBJECT_IDs and have the same sex values. Please correct the file and resubmit. |
| Error |
E0516_Pedigree_Twin_Parents_Missing |
Parent IDs are missing for twins. These subjects have been marked as MZ twins. Mother and father IDs cannot be 0 or blank for siblings. Create dummy parent IDs if no ID is available. Also include mother and father IDs under the subject ID columns of both the Pedigree DS and Subject Consent DS. |
Monozygotic twins and multiples should be assigned the same MZ_TWIN_ID but different SUBJECT_IDs and have the same Mother and Father. The Mother and Father column cannot be 0 or blank for subjects that have a TWIN_ID. Please create Dummy Ids as necessary and resubmit file. |
| Error |
E0517_Pedigree_Sex_Value |
Acceptable sex values are M/Male/1 or F/Female/2 or UNK/Unknown/NULL. Correct sex values. |
The values of the sex column are expected to be M/Male/1 or F/Female/2 or UNK/Unknown/NULL. Please see pedigree section of submission guide. |
| Error |
E0518_Pedigree_Parent_Sex |
Male subjects are found in the mother column or Female subjects are found in the father column. Correct sex inconsistencies. |
Please enter the correct sex for the all subjects listed in parents columns or reassign relationships. |
| Error |
E0519_Sex_Value_Mismatch_Ped2SC |
The sex values between the Subject Consent DS and the Pedigree DS are not consistent. Make all sex values consistent between all datasets that have sex values for each subject ID. If there are a large number of discrepancies, this often indicates that the father and mother columns of the Pedigree DS are swapped. |
The Pedigree file and Subject Consent file have mismatched sex values. |
| Error |
E0520_Non_Rectangular_File |
Data Dictionary file is not rectangular and has no VALUES column. |
If the file is non-rectangular, it must have a VALUES column |
| Error |
E0601_Genotype_Discordance |
Sample IDs that belong to the same subject ID have different genotypes. Verify ID mapping in SSM DS with genotype sets. Either 1) update subject ID, or 2) remove inconsistent sample IDs, or 3) fix genotype file. |
EXPECTED DUPLICATES: Samples from the same subject or from MZ twins are expected to have identical or near-identical genotypes. |
| Error |
E0602_Genotype_Cryptic_Duplicate |
Samples with identical genotypes are linked to different subjects and are not declared to be MZ twins in the Pedigree DS. Either 1) remove unexpected duplicates from the SSM, or 2) link subjects with identical genotypes to the same MZ twin ID in the Pedigree DS if they are MZ twins, or 3) Update the subject ID in the SSM so that the sample IDs point to the same subject. |
UNEXPECTED DUPLICATES: Genotypes from different subjects are expected to reflect subjects’ relatedness (unrelated/1st degree relations/etc ). |
| Report |
E0603_GRAF_Relationship_Report |
Relationship file with all pairwise relationships (first and second degree) computed from genotypes: {{ attachment_file }}. |
Graf Relationship file was created. |
| Error |
E0701_Subject_Consent_Sex_Value |
Sex column in the Subject Consent {{ file_name }} column {{ sex_col }} has values that are not consistent the submission guide. Please correct this column to have the allowed values [M/Male/1 or F/Female/2 or UNK/Unknown/NULL] and resubmit. |
The values of the sex column are expected to be [M/Male/1 or F/Female/2 or UNK/Unknown/NULL]. Please see subject consent section of submission guide. |
| Warning |
E0702_Subject_Consent_Sex_Column_Missing |
The Subject Consent file {{ file_name }} does not have the sex column included as the third column. Please add this column with the values [M/Male/1 or F/Female/2 or UNK/Unknown/NULL]. |
The Subject Consent file does not have an included sex column |
| Report |
E0703_GRAF_Sex_Distribution |
GRAF Sex Distribution file for distribution of sex values in phenotype file(s) and genotype files(s): {{ attachment_file }} |
GRAF Sex report file was created. |
| Error |
E0704_GRAF_Sex_Discordance |
GRAF Sex Discordance detected. If the samples are known to have chromosomal anomalies or you have information that this error is not consistent with your analysis, you may provide a README file explaining the sex errors. Upload the README under 'Other files' with type 'Molecular Data' in the Submission Portal. Otherwise, correct the reported sex so that it is consistent with the genotypes. |
Inconsistency between reported sex of the sample and sex inferred from the genotype data. |
| Warning |
E0705_GRAF_Insufficient_XMarkers |
Genotype files lack sufficient X chromosome markers for dbGaP to determine subject's sex or check concordance between phenotype file(s) and genotype file(s). dbGaP will continue processing unless you inform us that this is not expected. |
Not enough information to create the graf sex output file. |
| Error |
E0801_Design_Description_Too_Short |
Design Description requires {{ MIN_DESCR_SIZE }} characters minimally. |
Design description should be more than {{ MIN_DESCR_SIZE}} characters. |
| Error |
E0802_Not_In_Controlled_Vocab |
The column should have values from the controlled vocabulary list. Look at Terms tab in the template file for allowed controlled vocabulary terms. |
Values for this column should only contain allowed controlled vocabulary terms. |
| Error |
E0803_Duplicate_Rows_In_Sequence_Metadata |
Duplicate rows found in sequence metadata file. Each row in sequence metadata should be unique. Remove duplicates and replace file. |
Duplicate rows not allowed in sequence metadata file. |
| Error |
E0804_Invalid_Checksum_Format |
MD5 checksum does not have either allowed characters or has incorrect length. |
MD5 Checksum format should conform to the 32 bit hexadecimal string. |
| Error |
E0805_Missing_Value |
All required columns in the template are REQUIRED and should have values. |
All required columns in the template are REQUIRED and should have values. |
| Error |
E0806_Missing_Column |
REQUIRED columns missing from the sequence metadata file. |
One or more REQUIRED columns are missing on the sequence_data sheet of the sequence metadata file. |
| Error |
E0807_Duplicate_Values |
Multiple rows found with repeated checksum, file name or library_id values. One way to make the library_id value unique is to add the sample_id value to the end of library_id |
Each row must have a unique value for filename, checksum and library_id columns. |
| Error |
E0808_Sample_Not_Found |
Sample ID(s) in sequence metadata file was not found in Subject Sample Mapping file. |
Sample IDs in metadata file must be a subset of Sample IDs found in Subject Sample Mapping file. |
| Error |
E0809_Accession_Mismatch |
Study accession mismatch in submitted file. |
The study accession (phs######) in file must match exactly to the study for which the file is uploaded. |
| Warning |
E0810_Duplicate_Sample_Library_info |
Multiple rows found with same strategy, source and selection library info for the same sample ID. |
The study accession (phs######) in file must match exactly to the study for which the file is uploaded. |
| Report |
E0811_Sequence_Metadata_Load_Report |
Sequence Metadata file successfully loaded. Refer to attached file for more details: {{ attachment_file }} |
SRA metadata telemetry report created. |
| Error |
E0812_Sequence_Metadata_Load_Error |
Loading of the sequence metadata file failed. Refer to attached file for more details: {{ attachment_file }}. Fix errors and resubmit |
SRA metadata telemetry report created. |
| Error |
E0813_Invalid_Characters_In_Sequence_Metadata |
Invalid characters found in sequence metadata file. |
Invalid characters not allowed in sequence metadata file. |
| Error |
E0814_Sequence_Data_Files_Load_Error |
Loading of data files reported in sequence metadata failed. Fix errors and resubmit. Refer to attached file for more details: {{ attachment_file }}. |
Sequence data files are loaded. |
| Error |
E0815_Missing_Worksheet_From_Sequence_Metadata |
The submitted sequence metadata excel file is missing the {{ sheet_name }} worksheet |
Sequence metadata excel file must contain a worksheet named '{{ sheet_name }}' |
| Error |
E0816_DUPLICATED_SEQUENCE_DATA_FILES |
These files have been submitted previously. Each sequence data file (filename and md5) can only be submitted once for each study (including all versions). Fix errors and resubmit. |
The same sequence data file can be submitted only once for each study (including all versions). |
