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Accessing the Jobs Table
If you are currently running one or more pipelines, or have done so in the past, and wish to view the status and details of your pipeline jobs, you can do so by accessing the Jobs screen using the left navigation pane button shown below:
This will navigate to a tabular view of your present and past jobs, as depicted below.
Each row of this table corresponds to one job that you have submitted, and displays the following columns to give you a summary of each job:
| Name | This refers to the name of the pipeline that the job is running. For example, 'Antibody Annotator' or 'Alignment'. |
| Progress |
This column provides an estimate of the percentage completion of the job. Jobs that have terminated (successfully or otherwise) will always show a completion of 100%, and the color of the progress bar indicates whether the job was successful or not. Note that the percentage shown in this column is only an estimate and may not always be an accurate reflection of how much work remains. Some pipelines are better at reporting their progress than others, however we are always looking to improve progress reporting where possible. |
| Job Insights | Displays Insights about the job if there are any. This updates while the job is running, and can be useful for troubleshooting. You can also access the Job Details by mousing over an Insight. |
| Status | The current Status of the job. Possible statuses are listed below in detail. |
| Results | Has a clickable link to the result(s). In the case of the Export pipelines, this will be a download link that you can click on to download your exported data. Download links for Export results are currently available for up to 30 days following job completion. |
| Input Folder | Displays the name of (and a link to) the folder from which the job was run. |
| Last Updated | Displays the timestamp of the last update to this job. If your job is still Running or Queued and this timestamp has not been updated for several hours (or even days), then we would encourage you to get in touch with us to determine if there is a problem with the job. |
| Parameters | Displays the raw parameters of the job in JSON format. These are more easily viewed in the Details View. |
Job Status
As shown by the 'Status' column in the Jobs table, a job may exist in one of the following statuses:
- Queued - this means your job submission has been received and is currently waiting for Geneious Biologics to schedule and start the job. This may happen if you are running multiple large annotation jobs, or if others in your organisation are running multiple large jobs. In general, small jobs will not be queued.
- Running - your job is now executing and may periodically provide updates on its progress.
- Completed - your job has successfully completed and all results are available for viewing.
- Failed - your job has encountered an error and was unable to complete. The full error message can be found in the Details view.
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Cancelled - your job has been cancelled (either by you or another authorized party).
Job Insights
Biologics will also generate insights/notes for certain analysis jobs, which may provide valuable information about the current status of your job, or suggestions to troubleshoot your options if some settings look "off". Not all jobs will provide insights, but some of our annotation/analysis options will.
Clicking on the insight icon will display the findings:
You can also bring up the Job Details page (more below) when viewing the insight.
Job Details
To view more details of a job, select a single job in the Jobs table and click on the Details button (shown below).
You will then be shown the Details view for the selected job, as below.
The Details screen currently provides the following additional detail:
- Queued at: Date and time the job entered the queue
- Started at: Date and time the job started running
- Started by: The user that started the job
- Input files: A list of input files
- Reference Sequences (if applicable): The reference database(s) used
- Output files: A list of output files
- Job parameters - the full job parameters, rendered in JSON format. This information can be useful for troubleshooting purposes (when communicating with the support team) or may allow you to compare parameters across jobs. Note that these parameter names might differ slightly compared to the options shown in the pipeline options dialog.
- Status Updates - this is a list of all status updates recorded for your job, in descending order of timestamp. If your job has failed, you will be able to see the full error message at the top of this list.
Note that you can also view job parameters and history in the Info tab of any result.
You can also 'Report a problem' with your job from the Details view by clicking on the button below Status Updates. For more information on this, please see our Submitting Feedback article.
To navigate back to the Jobs table from this view, simply click on the 'Back' button, or use the left navigation pane.
Cancelling a Job
You can choose to cancel a job at any time while it is running. This can be helpful if you have started a job by accident using the wrong data or incorrect options, or if the job is taking unexpectedly long. To cancel, simply select the job that you wish to cancel in the table and click on the 'Cancel' button, as shown below.
You will be prompted for confirmation before proceeding, in case you selected the wrong job or accidentally clicked Cancel.
Note that you can only cancel a job that is in either the Queued or Running state. After submitting the cancellation, you should see the job's status transition to Cancelled. Any resources that were used for running the job will then be freed up for running other pending jobs.
Troubleshooting
Why has my job been in the Queued state for so long?
The two most likely reasons for this are:
- Geneious Biologics is responding to high demand by allocating additional resources to run your job. This allocation of resource may (in the worst case) take several minutes. If you are still waiting after several minutes, then it may be because...
- In order to ensure that Geneious Biologics remains responsive and available to all users, we may need to enforce limits on the number of jobs that can be running concurrently. If users in your organization are running a large number of jobs, or there are many jobs running across the system as a whole, then your jobs may need to queue for longer in order to ensure that those limits are respected.
In general, quick jobs, such as running an alignment on a small number of sequences, will be given priority in the system and will not have to queue for long (if at all).
If you feel that your jobs are queuing for an unreasonable length of time, even when your organization is not running a large number of jobs, please reach out to our support team so that we can investigate further, as we are always striving to eliminate any unnecessary delays in your workflow.
My job is Running, but why is the progress not updating?
Whilst we are always looking to improve the amount of feedback that our pipelines provide back to the user, there are some cases where it is not yet as regular or detailed as we would like. For pipelines run on large NGS data sets, our algorithms may sometimes be very busy performing intensive computation for hours or even days, and may not provide regular progress updates during this time, despite making significant progress in processing the data.
Additionally, the nature of biological data that Geneious Biologics processes is continually changing and expanding, as are the experimental techniques and analytical approaches employed by its user base. If you have any concerns about the efficacy or efficiency of our pipelines in your workflow, we would welcome and encourage you to engage with our support team so that we can better understand what you are trying to achieve with your data and how we can make Geneious Biologics work better (and faster) for you.