Pipeline run errors
Use this reference to identify and resolve errors that occur when the Emedgene pipeline processes a case. Each entry includes the numeric error code, the exception name, and a description of the likely cause and recommended corrective action.
Error code ranges
6XXX
Pipeline exceptions
8XXX
Infrastructure-related exceptions
9XXX
Sanity check exceptions
10XXX
Input-related exceptions (detailed below)
Input errors
These errors occur when case inputs — such as sample type, phenotypes, reference genome, or kit BED file — are missing, conflicting, or invalid.
10001
InputValidationException
One or more input fields failed validation. Check that all required case fields are filled in correctly before resubmitting.
10002
MissingInputFilesException
Expected input files were not found in the specified location. Verify that all files are accessible at the provided paths.
10003
FileNotFoundException
A required file could not be located. Confirm the file path is correct and that the file exists in the configured storage.
10004
BadPosException
A genomic position in the input is invalid or out of range for the reference genome.
10005
BadRefException
A reference allele in the input does not match the configured reference genome.
10006
MalformedTestDataException
The test data provided for the case is malformed or does not meet the expected format.
10007
NoneSampleTypeException
No sample type was specified. A sample type is required to run the pipeline.
10008
TooManyPhenotypesException
The number of phenotypes submitted exceeds the supported limit.
10009
NoSampleNameGivenException
A sample was submitted without a name. All samples must have a unique identifier.
10010
UnsupportedReference
The reference genome specified is not supported. See Supported reference genome assemblies for valid options.
10011
ReferenceConflictException
The input files reference conflicting genome assemblies. All files in a case must use the same reference genome.
10012
MissingKitBedException
A kit BED file is required for this case type but was not provided.
10013
UnknownHaplotypeException
A haplotype specified in the input is not recognized by the pipeline.
10014
HaplotypeAlleleAmountMismatchException
The number of alleles specified for a haplotype does not match the expected count.
File errors
These errors indicate a problem with a submitted file — it may be corrupted, empty, or unsorted.
10101
CorruptedFileException
A file could not be read because its contents are corrupted. Re-upload the file and resubmit.
10102
CorruptedGzipFileException
A gzip-compressed file is corrupted or was not compressed correctly. Re-compress and re-upload the file.
10103
EmptyFileException
A required file was found but contains no data. Ensure the correct non-empty file was uploaded.
10104
UnsortedInputFileException
An input file is not sorted in the required order. Sort the file by chromosome and position before resubmitting.
10105
EmptyRemoteFileException
A file retrieved from remote storage returned no data. Check that the file exists and is not empty at the remote location.
VCF errors
These errors are raised when the pipeline parses the VCF file and encounters structural problems, missing headers, unrecognized variant callers, or allele mismatches.
10201
CorruptedVcfException
The VCF file is corrupted and cannot be parsed. Validate the file with a VCF linter and re-upload.
10202
NoContigsException
The VCF header is missing contig definitions. Add ##contig lines for all chromosomes referenced in the file.
10203
NoTitleException
The VCF is missing the required #CHROM header line.
10204
NoVcfVersionException
The VCF header does not specify a file format version (##fileformat). Add a valid ##fileformat line.
10205
NoVariantsFound
The VCF file contains no variant records. Confirm the correct file was uploaded.
10206
UnsupportedVcfVersionException
The VCF format version is not supported. See Supported variant callers for compatible formats.
10207
ConflictingVariantTypesException
The VCF contains variants of conflicting types that cannot be processed together in a single run.
10208
SampleNameNotFoundInVcfException
The sample name specified for the case was not found in the VCF header. Verify the sample name matches exactly.
10209
MoreThanOneVarCallerMatched
The VCF matches more than one supported variant caller profile. Ensure the file originates from a single caller.
10210
CorruptedVariantException
One or more variant records in the VCF are malformed or missing required fields.
10211
CorruptedSVVariantException
One or more structural variant records are malformed. Check SV-specific fields such as SVTYPE and END.
10212
MissingVcfColumnException
A required VCF column is absent. Ensure the file includes all mandatory columns (CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO).
10213
NoEmedgenizerException
The pipeline could not identify the variant caller as a supported one for this VCF.
10214
ReferenceAlleleMismatchException
The REF allele in the VCF does not match the reference genome at the specified position.
10215
NoJSONEmedgenizerException
No compatible JSON-based variant caller annotation tool was identified for this VCF.
VCF line errors
These errors occur at the individual record level within a VCF file — malformed lines, missing fields, or ambiguous variant type annotations.
10301
CorruptedLineException
A line in the VCF file is malformed and could not be parsed. Check for encoding issues or unexpected characters.
10302
CorruptedHeaderException
A header line in the VCF is malformed. Validate all ##INFO, ##FORMAT, and ##FILTER header definitions.
10303
EmptyLineException
An unexpected empty line was found in the VCF body. Remove blank lines from within the file.
10304
MissingAltException
A variant record is missing the ALT allele field. All variants must have at least one ALT value.
10306
UnfinishedLineException
A line in the VCF appears truncated. The file may have been interrupted during upload or compression.
10307
MoreThanOneVariantTypeMatchedException
A single VCF line matched more than one variant type. Ensure variant records have unambiguous type annotations.
10308
CorruptedSampleColumnException
A sample column in the VCF is corrupted or does not match the FORMAT definition.
10309
CorruptedFormatForSampleException
The FORMAT field for a sample column is invalid or does not conform to the declared FORMAT header.
10310
InfinityVcfException
A numeric field in the VCF contains an infinity value, which is not permitted.
10311
MoreThanOneJSONVarCallerMatched
More than one JSON-based variant caller matched in this json line.
FASTQ errors
This error indicates a problem with a submitted FASTQ file.
10401
CorruptedFastqException
The FASTQ file is corrupted and cannot be parsed. Validate the file and re-upload a complete, intact copy.
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