How to Provide Log Files

How to Provide Log Files

To help the Seqera Labs Support Team resolve issues effectively, it’s essential to share relevant log files with your ticket submission. Add these logs as attachments to your ticket. The types of logs we may request include:

• Workflow/Run logs

  • Nextflow logs

  • Fusion logs

• Seqera Platform logs

  • Backend logs

  • Cron logs

  • Frontend logs

  • Groundswell

  • Redis logs

Nextflow Logs and Fusion Logs

Nextflow logs and Fusion can be retrieved directly from your Seqera Platform  instance by following these steps:

1. Log into Seqera Platform instance and click Runs.

2. Select the workflow you want to share.

3. Navigate to the Execution Log tab.

4. Click the Download Log Files dropdown and select Nextflow Log File.

5. Optionally, include the Nextflow Console Output for a complete view of the standard output.

Seqera Platform Logs

Seqera Platform logs are located on your deployment instance. The steps to retrieve these logs vary depending on your deployment type.

For Docker Compose Deployments

1. Log into your instance where the containers are running.

2. Identify the target container:

   docker ps

   Note the container ID or name (e.g., ba54613516f or Seqera_platform_backend_1).

3. Retrieve logs from the container:

   • To get full logs from the beginning:

     docker logs Seqera_platform_backend_1 > /tmp/backend.log

   • To get logs for a specific date:

     docker logs Seqera_platform_backend_1 | grep Sep-07 > /tmp/backend.log

4. Attach the generated backend.log file to your ticket.

5. Repeat this process for frontend, backend, and cron logs as needed. Use unique filenames (e.g., frontend.log, cron.log) to avoid overwriting existing files.

For Kubernetes-Based Deployments

1. Log into your instance where the Kubernetes pods are running.

2. Identify the target pods for log extraction:

   kubectl get pod -n [namespace]

3. Retrieve logs from a specific pod:

   kubectl logs [pod-name] -n [namespace] > /tmp/backend-pod.log

4. If requested, provide the pod’s deployment details:

   kubectl describe [pod-name] -n [namespace] > /tmp/describe-backend-pod.log

5. Use unique filenames for logs to avoid overwriting existing files.

Troubleshooting

In some cases, you may encounter issues downloading Nextflow logs through the Seqera Platform. If this happens, logs can also be retrieved from the work directory specified in the Compute Environment configuration.

Work Directory Retrieval

• Azure: Locate the work directory defined in your Azure Compute Environment settings.

• AWS Batch: Locate the work directory as specified in your Batch Compute Environment settings.

• GCP:  Locate the work directory as specified in your Batch Compute Environment settings.

These steps apply to all compute environments.