Task lifecycle in a HealthOmics run

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A task is a single process within a run. HealthOmics maps each task in your workflow to an omics computing instance type that best fits the task's required resources. You specify the required resources in the workflow definition. For more information, See Compute and memory requirements for HealthOmics tasks.

HealthOmics provides temporary run storage for the task to use. HealthOmics copies the task input files to the temporary run storage as read-only files. HealthOmics provides symbolic links so that the task can access the input files from the working directory. The task has access only to the files that you declare in the workflow definition file.

Task status values

You can track the progress of a task by monitoring the task status. When you start a run, HealthOmics sets the task status to Pending for each task in the run. When the task starts and progresses through its lifecycle, HealthOmics updates the status value to reflect its current progress.

You can retrieve task status using any of the following methods:

• The HealthOmics console displays the status of each task in a run on the Run details page.

• The GetRunTask API operation returns the task status.

• You can monitor task status using EventBridge events. For more information, see Using EventBridge with AWS HealthOmics.

You can retrieve the current status of a task using the GetRunTask API operation. The HealthOmics console displays the status for each task in a run on the Run details page.

HealthOmics supports the following task status values:

Pending

Your task is in the queue, waiting to start. Tasks stay in pending for a brief period before they start.

• Tasks remain in pending after your account has reached the maximum number of concurrent tasks.

• Tasks remain in pending if the run is part of a run group that has reached any of its resource maximum values.

• You can adjust run priorities so that specific queued runs and their tasks start before other queued runs. For more information about run priority, see Run priority

Starting

HealthOmics is creating the task and provisioning the resources required for the task, such as the workflow task node.

Running

The task status is Running while HealthOmics is processing the task.

Stopping

After completing the task processing and exporting the output data, the task transitions to Stopping.

• HealthOmics deprovisions the workflow task node.

Completed

HealthOmics has finished processing the task and has transferred the output data to the run storage file system.

Failed

HealthOmics encountered an error while processing the task and didn't complete it.

• The task transitions to Stopping status (HealthOmics deprovisions the resources) and then to Failed status.

• If the error is a service error (5XX HTTP status code), and the workflow supports retries for this task, HealthOmics attempts to process the task again. HealthOmics assigns a new task ID to the retry.

Canceled

HealthOmics stops the task after a user-initiated request to cancel the run.

• The task transitions to Stopping status (HealthOmics deprovisions the resources) and then to Canceled status.

Troubleshooting workflow tasks

The following are best practices and considerations for troubleshooting your tasks.

• Task logs rely on STDOUT and STDERR being produced by the task. If the application used in the task doesn’t produce either of these, then there won't be a task log. To assist with debugging, use applications in verbose mode.

• To view the commands being run in a task along with their interpolated values, use the set -x Bash command. This can help determine if the task is using the correct inputs and identify where errors might have kept the task from running as intended.

• Use the echo command to output the values of variables to STDOUT or STDERR. This helps you confirm that they're being set as expected.

• Use commands like ls -l <name_of_input_file> to confirm that inputs are present and are of the expected size. If they aren't, this might reveal a problem with a prior task producing empty outputs due to a bug.

• Use the command df -Ph . | awk 'NR==2 {print $4}' in a tasks script to determine the space currently available to the task and help identify situations where you might need to run the workflow with additional storage allocation.

Including any of the preceding commands in a task script assumes that the task container also includes these commands and that they are on the path of the container environment.