Known Issues

The following are known issues that we are working to resolve.

General

• None

Platform GUI

Flow

• When linking samples, the link is created at the parent at the folder level of the files associated with the sample, effectively sharing all files in the folder containing the sample files.

• Samples created automatically from sequencing runs configured to deliver results to the platform will result in a new volume named based on the sample ID. Content in the sample volume will show alongside the content of the volume created for the project.

• For each pipeline run, a new volume is created with a named based on the run ID. The volume contents are shown in the Data section alongside the content of the volume created for the project. This may result in files/folders appearing to have the same name in the platform GUI.

• For short pipeline runs, the Resource Utilization may not show any results in the plot due to the utilization sample rate being longer than the duration of the step.

• Pipelines created in the GUI cannot be updated via the command-line interface.

• Pipelines created via the command-line interface do not show in the GUI.

• The pipeline editor shows a "Reference Data" input icon and allows the icon to be added to the editor. The Reference Data input type is not currently supported.

• When Tools in "Draft" status contained within an existing pipeline are updated, the pipeline is not automatically updated. This can lead to unexpected behavior when executing the pipeline such as log files not appearing in the UI and any updates made to the Tool not taking effect. To workaround, the pipeline must be updated and re-saved (can be as simple as moving an icon in the pipeline editor view).

Bench

• Upon launching a workspace, the "Access" tab may shows a login view. To resolve, clear your browser cache and retry.

Command-line Interface

• In rare cases, when a file upload fails, the CLI will freeze. To exit, use a Ctrl-C command or similar.

• On Windows OS, Folder Upload hangs and does not complete. To exit, use a Ctrl-C command or similar.

Data Management

• If you upload a file to AWS with a "//" in the object key, the file will not be indexed into GDS or accessible.

• If you upload a file to AWS with a "/" at the end of the object key, the file will not be indexed into GDS or accessible.

• There is occasionally a lag between file upload to S3 and its appearance in GDS. Contact Technical Support if you observe this.

Analysis

TES

• When insufficient resources are available for a task to be launched, the status of the task run will be "Running" and no status detail will be returned. This can occur when no F1 instances are available when FPGA is requested in the "Hardware" field, or sufficient resources are not available for the requested task.

• If the "Resources" object is specified in the body of a task run or task version, "CPU" and "Memory" are both required fields. These fields cannot be specified by substitutions and must be numeric.

• A trailing "/" is not allowed in an output "url". The task will fail due to a malformed path.

• When 2 or more consecutive "/" are included in an output "url" field, one of the "/" will be removed and the resulting path will be used as the output directory. Avoid including multiple "/" except after defining the protocol. For example: gds://testvolume/folder1//output --> will result in outputs written to gds://testvolume/folder1/output gds://testvolume/folder/output --> valid

• When more than one set of brackets is included in a field, the validation will forbid the desired action. Make sure that fields only contain the "" convention for substitution.

• It is possible that a task can be marked as completed before the output files are fully indexed into GDS. As a result, the files might not be available yet for download or use. This should be a rare occurrence. In the future, we plan to prevent a task from completing until all the files are fully available in GDS.

• When creating a task run and the user inputs a pre-signed url, TES will hide the pre-signed url. However if the user creates a task version with a pre-signed url as an input url, then TES will not hide the pre-signed url.

WES

• Nested sub-workflows are not supported.

Events

• None