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 and Track Analysis Delivery Statuses.

For information about sequencing yield status, see Yield.

Statuses in BaseSpace Sequence Hub

Status

Description

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 Payment—The analysis app purchase is in progress.
Payment Aborted—The analysis app purchase was canceled.
Payment Complete—The analysis app purchase is complete and the analysis can begin.
Pending—The analysis is waiting for dependencies (eg, yield or completion of another analysis) to be met.
Pending Execution—The analysis workflow has met its dependencies (eg, yield or completion of another analysis) and is looking for a machine to run on.
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.
Timed Out—The analysis did not complete within 48 hours and was terminated.
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.
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 YieldBaseSpace 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 YieldBaseSpace 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 to 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—There is an issue with the sample sheet associated with the run. The run can be requeued after the sample sheet is fixed.