# Statuses

BaseSpace Sequence Hub tracks the status of biosample data from library prep through sequencing and delivery of analysis files.

For information about changing statuses, see [Manual QC](https://help.connected.illumina.com/basespace/automate/manual-qc) and [Track Analysis Delivery Statuses](https://help.connected.illumina.com/basespace/collaborate/share-with-collaborators/track-analysis-delivery-status).

For information about sequencing yield status, see [Yield](https://help.connected.illumina.com/basespace/automate/yield).

## Analysis Delivery Status

*The delivery status of the analysis. Manually update statuses to track the progress of analysis deliverables.* Possible values are:

* On Hold—The analysis is not ready for delivery.
* Do Not Deliver—The analysis files should not be delivered. You can use this status to confirm that a QC Failed analysis has been reviewed and should not be delivered, or to mark R\&D and test analyses that are for internal use only.
* Deliver—The analysis files can be delivered.
* Ready For Delivery—The analysis files have been reviewed and are ready for delivery.
* Delivery in Progress—The analysis files are currently being transferred.
* Delivery Failed—Delivery of the analysis was attempted and failed.
* Delivered—The analysis files have been delivered.

## Analysis Status

*The status of the analysis through execution and QC.* Possible values are:

* Pending—The analysis is waiting for dependencies (eg, yield or completion of another analysis) to be met.
* Queued for Analysis—The analysis workflow has met its dependencies (eg, yield or completion of another analysis) and is queued for analysis. Analyses with this status cannot be deleted.
* Awaiting Authorization—The analysis has been created but has not been accepted.
* Initializing—The app has launched and is awaiting execution.
* Running—The analysis is running. Analyses with this status cannot be deleted.
* Timed Out—The analysis did not complete within its designated time limit. Depending on the app, this is typically 4-7 days.
* Needs Attention—There is a problem with the run sample sheet.
* Canceled—A user manually canceled the analysis before its dependencies were met.
* Aborting—The analysis is in the process of being stopped. Analyses with this status cannot be deleted.
* Aborted—The analysis has been stopped.
* Complete—The analysis has finished and is ready for use.
* QC Passed—All analysis metrics met established thresholds or were reviewed and manually passed.
* QC Failed—One or more analysis metrics did not meet established thresholds or were reviewed and manually failed.
* Discarded—The QC Failed analysis has been reviewed and can be ignored.

## Biosample Status

*Higher-level status of the biosample, from library preparation through sequencing. If more than one library has been prepared from a biosample, the status refers to the most recent library being processed.* Possible values are:

* New—The default state for a biosample created by LIMS systems.
* Active—The biosample is being worked on in the lab. The default state for a biosample created by non-LIMS systems.
* Done—The analysis files have been delivered. This status is set manually
* Canceled—The biosample is canceled and will no longer be used or processed.
* QC Failed—The biosample has failed Automatic QC in a LIMS system or was manually failed based on metrics.
* On Hold—The biosample needs attention or further review. This status is set manually.

## Biosample Lab Status

*The status of lab tasks for the biosample, from library preparation through sequencing. If more than one library has been prepared from a biosample, the status refers to the most recent library being processed. Statuses are automatically updated by BaseSpace Sequence Hub.* Possible values are:

* New—The biosample has been added to BaseSpace Sequence Hub. This is the default status.
* Visual QC Failed—The container of biosamples failed visual inspection quality control check and cannot continue.
* Visual QC Passed—The container of biosamples passed visual inspection quality control check.
* Quant QC Failed—The biosample did not meet concentration threshold at the quantification step.
* Quant QC Passed—The biosample met concentration threshold at the quantification step.
* Sequencing—The biosample is being sequenced by an instrument.
* Requeued—A requeue for the biosample or library has been initiated and acknowledged by the lab.
* Missing Yield—BaseSpace Sequence Hub has not received the required yield before the process has timed out.
* Complete—The required yield for the biosample has been met.

## FASTQ Status

*The status of the generated or uploaded FASTQ dataset.*

* Default status for FASTQ data. Datasets in the default state are included in data aggregation for analysis.
* QC Passed—The FASTQ data passed QC.
* QC Failed—The FASTQ data failed QC.

## Lab Requeue Status

*The status of the requeue.* Possible values are:

* Pending—The requeue request has been initiated and is awaiting acknowledgment by a lab or LIMS.
* Acknowledged—The requeue request has been acknowledged manually by a lab or automatically by a LIMS.
* Canceled—The requeue has been stopped manually by a user.
* Expired—The requeue has been acknowledged but has not met the minimum yield required within the configured amount of time.
* Fulfilled—The requeue has met the requested yield.
* Failed—The requeue request has been rejected because there is not enough volume to perform the requeue.

## Lane Status

*The status of the individual lane. Lane status can be changed by Automatic Lane QC, manually, or via API.* Possible values are:

* QC Passed—The lane data passed QC.
* QC Failed—The lane data failed QC.

## Lane and QC Status

*The overall status of the lanes on a run.* Possible values are:

* Initial—The default status for a lane until QC has been performed or is manually overwritten.
* Lane Pending QC—Automatic lane QC is being processed against the run thresholds (set via an API).
* Lane QC Failed—The lane has failed the automatic QC thresholds set by the user (via an API) or has been manually overwritten.
* QC Passed—All lanes passed QC.
* Rehybed—The run has been stopped because of a problem with the flow cell. After the flow cell is rehybed, it is used in a new run.

## Library Status

*The status of the library. Library status is updated via the BaseSpace Sequence HubAPI.* Possible values are:

* Active—The default status of a library.
* Canceled—The library has been marked as canceled and will no longer be worked on.
* Failed—The library has failed QC metrics.
* Consumed—The library has exhausted its volume and can no longer be requeued.

## Pool Status

*The status of the pool. Pool status is updated via the BaseSpace Sequence HubAPI.* Possible values are:

* QC Passed—The data from the pool has passed QC. This is the default status.
* QC Failed—The data from the pool do not pass QC.
* Failed—The pool failed due to contamination or other physical reason.
* Consumed—The pool contents have been used and there is not enough volume for a requeue.
* Requeued—A requeue has been initiated for the pool.

## Prep Request Status

* Active—A library kit and yield are specified in an imported biosample workflow file.
* Missing Yield—BaseSpace Sequence Hub has not received the required yield before the yield timeout.
* Canceled—The request to sequence the library has been canceled.

## Run Status

*The status of the sequencing run: from Prep Tab planning, sequencing, file-upload, and FASTQ analysis.* Statuses are automatically updated from the instrument.

### Prep Tab statuses

* Planning—The run is being planned in the Prep Tab.
* Ready—The run prepared on the Prep Tab is ready to be sequenced.
* Unknown—The status of the run is unknown.

### Sequencing statuses

* Running—The instrument is sequencing the run.
* Paused—A user paused the run on the instrument control software.
* Stopped—The instrument has been put into a Stopped state through the instrument control software.

### File Upload and Analysis statuses

* Uploading—The instrument completed sequencing and is uploading files.
* Failed Upload—The instrument failed to upload files to the BaseSpace Sequence Hub.
* Pending Analysis—The file has uploaded completely and is waiting for the Generate FASTQ analysis to begin.
* Analyzing—The Generate FASTQ analysis is running.
* Complete—The sequencing run and subsequent Generate FASTQ analysis completed successfully.
* Failed—Either the sequencing run was failed using the instrument control software or Generate FASTQ failed to complete.
* Rehybing—A flow cell has been sent back to a cBot for rehybing. When the new run is complete, the rehybing status is changed to Failed.
* Needs Attention—There is an issue with the sample sheet associated with the run. The run can be requeued after the sample sheet is fixed.
* Timed Out—The sequencing run did not finish sequencing, uploading, or analyzing within 14 days and was automatically timed out.