> 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/reviewing_a_case/case_status/case-progress-indicator-v100.40.0+.md).

# Case progress indicator (v100.40.0+)

Use the case progress indicator to determine where a case is in the analysis workflow and whether you need to take action.

The indicator appears in the **Status** column on the **Cases page** for cases with **In progress**, **Re-Analysis**, or **Issue reported** status.

***

## Case progress indicator meaning

This section explains what each progress indicator state means for cases with **In progress** or **Re-Analysis** status.

### 1. Secondary analysis running

{% columns %}
{% column width="33.33333333333333%" valign="middle" %}

<div align="center"><figure><img src="/files/em75RVFr9i4Y84Frqemu" alt=""><figcaption><p>Secondary analysis running</p></figcaption></figure></div>
{% endcolumn %}

{% column width="66.66666666666667%" valign="middle" %}
**Indicator:** Grey striped progress bar.

**Meaning:** The FASTQ‑based case is running DRAGEN secondary analysis.
{% endcolumn %}
{% endcolumns %}

### 2. Queued

{% columns %}
{% column width="33.33333333333333%" valign="middle" %}

<div align="center"><figure><img src="/files/2iNQ3hd6FfJD9NjIC4pJ" alt=""><figcaption><p>Queued</p></figcaption></figure></div>
{% endcolumn %}

{% column width="66.66666666666667%" %}
**Indicator:** Empty segmented progress bar.

**Meaning:** The system has accepted the VCF (either a VCF case or the VCF output from integrated DRAGEN secondary analysis), but processing has not started yet.
{% endcolumn %}
{% endcolumns %}

### 3. Tertiary analysis running

Blue segments fill from left to right as the case moves through the five stages of the Emedgene tertiary analysis pipeline.

* A filled blue segment indicates a completed stage
* A half-filled blue segment indicates the stage in progress

{% columns %}
{% column width="41.66666666666667%" valign="middle" %}

<div align="center"><figure><img src="/files/HNPhLnFlfTbyr830ocW1" alt=""><figcaption><p>Tooltip showing current stage, elapsed time, and estimated total processing time</p></figcaption></figure></div>
{% endcolumn %}

{% column width="58.33333333333333%" %}
Hover over the indicator to view:

* The current tertiary analysis stage
* Elapsed time since tertiary analysis started
* Estimated total processing time (when available).
  {% endcolumn %}
  {% endcolumns %}

#### 3.1. Normalization

{% columns %}
{% column width="33.33333333333333%" valign="middle" %}

<div align="center"><figure><img src="/files/56kJHOAdbYvYafyRBh00" alt=""><figcaption><p>Normalization</p></figcaption></figure></div>
{% endcolumn %}

{% column width="66.66666666666667%" valign="middle" %}
**Indicator:** Segment 1 is half-filled.

**Meaning:** The system standardizes and prepares the uploaded data for downstream processing.
{% endcolumn %}
{% endcolumns %}

#### 3.2. Annotation

{% columns %}
{% column width="33.33333333333333%" valign="middle" %}

<div align="center"><figure><img src="/files/gAuzwE5FGq7JRa3Z012r" alt=""><figcaption><p>Annotation</p></figcaption></figure></div>
{% endcolumn %}

{% column width="66.66666666666667%" valign="middle" %}
**Indicator:** Segment 1 is filled and segment 2 is half-filled.

**Meaning:** Variants are enriched with genomic, clinical, population, transcript, phenotype, and knowledge base annotations.
{% endcolumn %}
{% endcolumns %}

#### 3.3. Indexing

{% columns %}
{% column width="33.33333333333333%" valign="middle" %}

<div align="center"><figure><img src="/files/Vyf4t5ZqmCdMEfnioG9g" alt=""><figcaption><p>Indexing</p></figcaption></figure></div>
{% endcolumn %}

{% column width="66.66666666666667%" valign="middle" %}
**Indicator:** Segments 1-2 are filled and segment 3 is half-filled.

**Meaning:** The annotated data is indexed to prepare the case for review within the platform.
{% endcolumn %}
{% endcolumns %}

#### 3.4. Quality check

{% columns %}
{% column width="33.33333333333333%" valign="middle" %}

<div align="center"><figure><img src="/files/gykR56ixMaLIg348jUUo" alt=""><figcaption><p>Quality check</p></figcaption></figure></div>
{% endcolumn %}

{% column width="66.66666666666667%" valign="middle" %}
**Indicator:** Segments 1-3 are filled and segment 4 is half-filled.

**Meaning:** The system performs quality validation.
{% endcolumn %}
{% endcolumns %}

#### 3.5. AI Shortlist

{% columns %}
{% column width="33.33333333333333%" valign="middle" %}

<div align="center"><figure><img src="/files/XGLWwiQ5RZNeQ1G7BAS1" alt=""><figcaption><p><strong>AI Shortlist</strong></p></figcaption></figure></div>
{% endcolumn %}

{% column width="66.66666666666667%" valign="middle" %}
**Indicator:** Segments 1-4 are filled and segment 5 is half-filled.

**Meaning:**

* The system performs AI-driven phenotype matching.
* The **AI Shortlist** performs variant prioritization, resulting in the list of [Most Likely Candidates and Candidates](/emedgene/emedgene-analyze-manual/reviewing_a_case/candidates-tab/most_likely_candidates_and_candidates.md) for the case.
  {% endcolumn %}
  {% endcolumns %}

After all five tertiary analysis stages complete, the case status changes to **Delivered.**

***

## Case processing failure

In case of processing failure, **Issue reported** status may be supplemented with the progress indicator.

### Secondary analysis failure

{% columns %}
{% column width="33.33333333333333%" valign="middle" %}

<div align="center"><figure><img src="/files/XAkVFSR6fKRMTxDEidJA" alt=""><figcaption><p>Secondary analysis failure</p></figcaption></figure></div>
{% endcolumn %}

{% column width="66.66666666666667%" valign="middle" %}
**Indicator:** Red striped progress bar.

**Meaning:** Failure during DRAGEN secondary analysis.
{% endcolumn %}
{% endcolumns %}

### VCF file validation failure

**Indicator:** No progress indicator is shown.

**Meaning:** Input VCF file issues.

### Tertiary analysis failure

{% columns %}
{% column width="33.33333333333333%" valign="middle" %}

<div align="center"><figure><img src="/files/oSddoo57i2y4w1Akj8iP" alt=""><figcaption><p>Tertiary analysis failure at Quality check stage</p></figcaption></figure></div>
{% endcolumn %}

{% column width="66.66666666666667%" %}
**Indicator:** Progress bar shows completed tertiary analysis stages in blue and the failed stage in red.

**Meaning:** Processing stopped during the stage corresponding to the segment filled in red.
{% endcolumn %}
{% endcolumns %}

Hover over the indicator to confirm the failed stage. Select the question-mark icon (<i class="fa-circle-question">:circle-question:</i>) to view error details.

<div align="center"><figure><img src="/files/ppUPsrncWB3mAUEfcfDk" alt=""><figcaption><p>Tertiary analysis failure indicator</p></figcaption></figure></div>

## Learn more

<table data-view="cards"><thead><tr><th></th><th></th><th></th></tr></thead><tbody><tr><td><strong>Case status</strong></td><td>Overview of case status behavior, history, and related workflows.</td><td><i class="fa-up-right-from-square">:up-right-from-square:</i> <a href="/pages/VIUNnrtei5oMuQ3EK59b">Learn more</a></td></tr><tr><td><strong>Case statuses in a case lifecycle</strong></td><td>Review status transitions, control types, and the reference status list.</td><td><i class="fa-up-right-from-square">:up-right-from-square:</i> <a href="/pages/7dMkh6Debg84ISFWnfCH">Learn more</a></td></tr><tr><td><strong>How to update a case status</strong></td><td>Change the current case status from the case page or the Cases table.</td><td><i class="fa-up-right-from-square">:up-right-from-square:</i> <a href="/pages/2puvLO2kJ6Rb9EEaM5WM">Learn more</a></td></tr><tr><td><strong>Case status management</strong></td><td>Create custom statuses and reorder them for your organization.</td><td><i class="fa-up-right-from-square">:up-right-from-square:</i> <a href="/pages/XB7boIzEhQCcUvBDG8v1">Learn more</a></td></tr></tbody></table>


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