> For the complete documentation index, see [llms.txt](https://help.connected.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/troubleshooting/pipeline-run-errors.md).

# 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.

{% hint style="info" %}
When a pipeline run fails, the error code is shown on the case card and in the case details. Locate the code in the relevant section below to understand the cause and next step. If the code is not listed, or if the issue persists, contact Illumina Technical Support with the error code, the case ID, and any relevant logs.
{% endhint %}

***

### Error code ranges

<table data-search="false"><thead><tr><th>Code range</th><th>Category</th></tr></thead><tbody><tr><td><code>6XXX</code></td><td>Pipeline exceptions</td></tr><tr><td><code>8XXX</code></td><td>Infrastructure-related exceptions</td></tr><tr><td><code>9XXX</code></td><td>Sanity check exceptions</td></tr><tr><td><code>10XXX</code></td><td>Input-related exceptions (detailed below)</td></tr></tbody></table>

***

### Input errors

These errors occur when case inputs — such as sample type, phenotypes, reference genome, or kit BED file — are missing, conflicting, or invalid.

<table data-search="false"><thead><tr><th>Code</th><th width="237.3515625">Exception</th><th>Description</th></tr></thead><tbody><tr><td>10001</td><td>InputValidationException</td><td>One or more input fields failed validation. Check that all required case fields are filled in correctly before resubmitting.</td></tr><tr><td>10002</td><td>MissingInputFilesException</td><td>Expected input files were not found in the specified location. Verify that all files are accessible at the provided paths.</td></tr><tr><td>10003</td><td>FileNotFoundException</td><td>A required file could not be located. Confirm the file path is correct and that the file exists in the configured storage.</td></tr><tr><td>10004</td><td>BadPosException</td><td>A genomic position in the input is invalid or out of range for the reference genome.</td></tr><tr><td>10005</td><td>BadRefException</td><td>A reference allele in the input does not match the configured reference genome.</td></tr><tr><td>10006</td><td>MalformedTestDataException</td><td>The test data provided for the case is malformed or does not meet the expected format.</td></tr><tr><td>10007</td><td>NoneSampleTypeException</td><td>No sample type was specified. A sample type is required to run the pipeline.</td></tr><tr><td>10008</td><td>TooManyPhenotypesException</td><td>The number of phenotypes submitted exceeds the supported limit.</td></tr><tr><td>10009</td><td>NoSampleNameGivenException</td><td>A sample was submitted without a name. All samples must have a unique identifier.</td></tr><tr><td>10010</td><td>UnsupportedReference</td><td>The reference genome specified is not supported. See Supported reference genome assemblies for valid options.</td></tr><tr><td>10011</td><td>ReferenceConflictException</td><td>The input files reference conflicting genome assemblies. All files in a case must use the same reference genome.</td></tr><tr><td>10012</td><td>MissingKitBedException</td><td>A kit BED file is required for this case type but was not provided.</td></tr><tr><td>10013</td><td>UnknownHaplotypeException</td><td>A haplotype specified in the input is not recognized by the pipeline.</td></tr><tr><td>10014</td><td>HaplotypeAlleleAmountMismatchException</td><td>The number of alleles specified for a haplotype does not match the expected count.</td></tr></tbody></table>

***

### File errors

These errors indicate a problem with a submitted file — it may be corrupted, empty, or unsorted.

| Code  | Exception                  | Description                                                                                                                |
| ----- | -------------------------- | -------------------------------------------------------------------------------------------------------------------------- |
| 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.

<table data-search="false"><thead><tr><th>Code</th><th>Exception</th><th>Description</th></tr></thead><tbody><tr><td>10201</td><td>CorruptedVcfException</td><td>The VCF file is corrupted and cannot be parsed. Validate the file with a VCF linter and re-upload.</td></tr><tr><td>10202</td><td>NoContigsException</td><td>The VCF header is missing contig definitions. Add ##contig lines for all chromosomes referenced in the file.</td></tr><tr><td>10203</td><td>NoTitleException</td><td>The VCF is missing the required #CHROM header line.</td></tr><tr><td>10204</td><td>NoVcfVersionException</td><td>The VCF header does not specify a file format version (##fileformat). Add a valid ##fileformat line.</td></tr><tr><td>10205</td><td>NoVariantsFound</td><td>The VCF file contains no variant records. Confirm the correct file was uploaded.</td></tr><tr><td>10206</td><td>UnsupportedVcfVersionException</td><td>The VCF format version is not supported. See Supported variant callers for compatible formats.</td></tr><tr><td>10207</td><td>ConflictingVariantTypesException</td><td>The VCF contains variants of conflicting types that cannot be processed together in a single run.</td></tr><tr><td>10208</td><td>SampleNameNotFoundInVcfException</td><td>The sample name specified for the case was not found in the VCF header. Verify the sample name matches exactly.</td></tr><tr><td>10209</td><td>MoreThanOneVarCallerMatched</td><td>The VCF matches more than one supported variant caller profile. Ensure the file originates from a single caller.</td></tr><tr><td>10210</td><td>CorruptedVariantException</td><td>One or more variant records in the VCF are malformed or missing required fields.</td></tr><tr><td>10211</td><td>CorruptedSVVariantException</td><td>One or more structural variant records are malformed. Check SV-specific fields such as SVTYPE and END.</td></tr><tr><td>10212</td><td>MissingVcfColumnException</td><td>A required VCF column is absent. Ensure the file includes all mandatory columns (CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO).</td></tr><tr><td>10213</td><td>NoEmedgenizerException</td><td>The pipeline could not identify the variant caller as a supported one for this VCF.</td></tr><tr><td>10214</td><td>ReferenceAlleleMismatchException</td><td>The REF allele in the VCF does not match the reference genome at the specified position.</td></tr><tr><td>10215</td><td>NoJSONEmedgenizerException</td><td>No compatible JSON-based variant caller annotation tool was identified for this VCF.</td></tr></tbody></table>

***

### VCF line errors

These errors occur at the individual record level within a VCF file — malformed lines, missing fields, or ambiguous variant type annotations.

<table data-search="false"><thead><tr><th>Code</th><th>Exception</th><th>Description</th></tr></thead><tbody><tr><td>10301</td><td>CorruptedLineException</td><td>A line in the VCF file is malformed and could not be parsed. Check for encoding issues or unexpected characters.</td></tr><tr><td>10302</td><td>CorruptedHeaderException</td><td>A header line in the VCF is malformed. Validate all ##INFO, ##FORMAT, and ##FILTER header definitions.</td></tr><tr><td>10303</td><td>EmptyLineException</td><td>An unexpected empty line was found in the VCF body. Remove blank lines from within the file.</td></tr><tr><td>10304</td><td>MissingAltException</td><td>A variant record is missing the ALT allele field. All variants must have at least one ALT value.</td></tr><tr><td>10306</td><td>UnfinishedLineException</td><td>A line in the VCF appears truncated. The file may have been interrupted during upload or compression.</td></tr><tr><td>10307</td><td>MoreThanOneVariantTypeMatchedException</td><td>A single VCF line matched more than one variant type. Ensure variant records have unambiguous type annotations.</td></tr><tr><td>10308</td><td>CorruptedSampleColumnException</td><td>A sample column in the VCF is corrupted or does not match the FORMAT definition.</td></tr><tr><td>10309</td><td>CorruptedFormatForSampleException</td><td>The FORMAT field for a sample column is invalid or does not conform to the declared FORMAT header.</td></tr><tr><td>10310</td><td>InfinityVcfException</td><td>A numeric field in the VCF contains an infinity value, which is not permitted.</td></tr><tr><td>10311</td><td>MoreThanOneJSONVarCallerMatched</td><td>More than one JSON-based variant caller matched in this json line.</td></tr></tbody></table>

***

### FASTQ errors

This error indicates a problem with a submitted FASTQ file.

| Code  | Exception               | Description                                                                                                |
| ----- | ----------------------- | ---------------------------------------------------------------------------------------------------------- |
| 10401 | CorruptedFastqException | The FASTQ file is corrupted and cannot be parsed. Validate the file and re-upload a complete, intact copy. |

<br>


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