Skip to main content

Remote Run Monitoring

Elembio Cloud synchronizes with connected systems to update run monitoring information in real time. Review the information on the following pages:

  • Active Runs: Summarizes information for the most recent runs, grouped by instrument.
  • All Runs: Displays information for active and historical runs from connected systems.
  • Run Details: Displays detailed information for a run.

Active Runs

Cards on the Active Runs page display high-level information about each active and recently finished sequencing run. The page orders the cards by instrument and side A or B, mimicking the instrument display. A dynamic gauge graphic on each card visualizes the run progress and the number of cycles completed, changing colors for different statuses.

The cards update as follows.

  • When a run is in progress, the card information updates in real time. The card links to the Run Details for the run.
  • When a run is no longer in progress, the card displays information for the last run executed. The card links to the Run Details for the run, and the card footer indicates the side is available.
  • The card always displays a badge for the most recent run status.

Figure 1: Example cards on an Active Runs page

Active Runs

Run Statuses

StatusGauge ColorDescription
Priming or PrimedBlueThe run is in setup mode. Metrics do not populate before sequencing starts.
SequencingBlueThe run is actively progressing. Metrics populate as they become available.
Pausing or PausedOrangeThe run is pausing or paused for flexible start. Resumption is automatic.
CompletedGreenThe run successfully finished. The instrument completed data transfer to the selected storage location.
FailedRedThe instrument encountered a critical issue during the run and cannot successfully finish. Data analysis completed up to and including the last successfully sequenced cycle, and the instrument transferred available data to the selected storage location.
StoppedTealA user stopped the run before it finished. Data analysis completed up to and including the last successfully sequenced cycle, and the instrument transferred all data to the selected storage location.

All Runs

The All Runs table displays a complete list of data for active and historical runs. Buttons filter runs, hide and show columns, and navigate table pages. The Run Name and Run ID fields link to the Run Details for the run.

Remove a Run

Remove a run to elimate the run from Elembio Cloud. Although a removed run no longer appears, the data remains archived and hidden. If you accidentally remove a run, contact Element Technical Support to restore it.

  1. On the All Runs page, locate the run you want to remove.
  2. In the Actions column, select More, and then select Remove.
  3. When prompted, enter the name of the run.
  4. Select Remove to immediately remove the run.

Run Details

A Run Details page displays the complete record of a sequencing run. The page includes the following features:

  • Run Overview: Visualizes the current run status in a gauge graphic.
  • Primary Analysis Metrics: Displays key run metrics, including reads, yield, Q30, and percent reads passing filter (%PF).
  • Run Setup: Displays run setup details.
  • Run Configuration: Displays detailed information about the run, cartridge, buffer bottle, and flow cell.
  • Primary Analysis: Graphs metrics, such as PhiX error rates and Q30, throughout Read 1 (R1) and Read 2 (R2).

Primary Analysis Charts

On the Primary Analysis tab, charts graph the following quality metrics throughout the run. Available metrics depend on the run setup and the version of AVITI Operating Software (AVITI OS).

Each chart includes buttons to expand the graph and export it as an image. If you are using the individually addressable lanes add-on, buttons let you view charts and metrics for Library Pool 1 or Library Pool 2.

ChartAVITI OS VersionDescription
Q-Scores
  • AVITI OS v1.0.0+ for Q30
  • AVITI OS v2.2.0+ for Q40 and average Q-score
The percentage of base calls with a Q-score ≥ Q30, a Q-score ≥ Q40, and the average Q-score for each cycle in Read 1 and Read 2.
  • Q30 indicates an incorrect base call probability of 1 in 1000, which equals a 99.9% confidence rate.
  • Q40 indicates an incorrect base call probability of 1 in 10,000, which equals a 99.99% confidence rate.
  • Average Q-score is the median Q-score.
PhiX Error Rate
  • AVITI OS v1.0.0+ for PhiX error rate
  • AVITI OS v2.2.0+ for % PhiX Aligned
The percentage of control reads that do not align to a spike-in of PhiX Control Library. The % PhiX Aligned metric appears at the top of the chart.
Elembio Cloud displays the chart only when the library pool includes a spike-in of PhiX Control Library.
Indexing Assignment
  • AVITI OS v2.0.0+ for chart
  • AVITI OS v2.4.0+ for top unassigned sequences
The percentages of reads assigned with a perfect index match or an index mismatch. Expanding the chart displays tables that list the top samples with a mismatch, unassigned sequences, and samples with low representation. The chart is only available for runs that include a run manifest with 1–768 index pairs across both lanes.
Base CompositionAVITI OS v2.2.0+The percentage of adenine (A), cytosine (C), guanine (G), and thymine (T) bases in each cycle of Read 1, Read 2, Index 1, and Index 2.
Image ThumbnailAVITI OS v2.2.0+The image thumbnail displays a snapshot of the polonies on a tile from the first cycle of Read 1. The image indicates sample density and loading concentration on the flow cell, providing a quality check to identify overloading or underloading.

Troubleshooting Run Monitoring

If Elembio Cloud data seem out-of-sync with instrument data, the instrument might have lost the network connection.

  1. Reconnect the instrument to the network, and then make sure that the data update in Elembio Cloud.
  2. If the issue persists, contact Element Technical Support.