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General troubleshooting

Common errors​

timeout is not an integer or out of range or ERR timeout is not an integer or out of range

This error can occur if you're using Seqera Platfrom v24.2 upwards and have an outdated version of Redis. From v24.2 Redis version 6.2 or greater is required. Follow your cloud provider specifications to upgrade your instance.

Unknown pipeline repository or missing credentials error from public GitHub repositories

GitHub imposes rate limits on repository pulls (including public repositories), where unauthenticated requests are capped at 60 requests/hour and authenticated requests are capped at 5000 requests/hour. Seqera Platform users tend to encounter this error due to the 60 requests/hour cap.

Try the following:

  1. Ensure there's at least one GitHub credential in your workspace's Credentials tab.

  2. Ensure that the Access token field of all GitHub credential objects is populated with a Personal Access Token value and not a user password. GitHub PATs are typically longer than passwords and include a ghp_ prefix. For example: ghp*IqIMNOZH6zOwIEB4T9A2g4EHMy8Ji42q4HA

  3. Confirm that your PAT is providing the elevated threshold and transactions are being charged against it:

    curl -H "Authorization: token ghp_LONG_ALPHANUMERIC_PAT" -H "Accept: application/vnd.github.v3+json" https://api.github.com/rate_limit

No such variable error

This error can occur if you execute a DSL1-based Nextflow workflow using Nextflow 22.03.0-edge or later.

Sleep commands in Nextflow workflows

The sleep commands in your Nextflow workflows may differ in behavior depending on where they are:

  • If used within an errorStrategy block, the Groovy sleep function will be used (which takes its value in milliseconds).
  • If used within a process script block, that language's sleep binary/method will be used. For example, this bash script uses the bash sleep binary, which takes its value in seconds.

Large number of batch job definitions

Platform normally looks for an existing job definition that matches your workflow requirement. If nothing matches, it recreates the job definition. You can use a simple bash script to clear job definitions. You can tailor this according to your needs, e.g., deregister only job definitions older than x days.

jobs=$(aws --region eu-west-1 batch describe-job-definitions | jq -r .jobDefinitions[].jobDefinitionArn)

for x in $jobs; do
  echo "Deregister $x";
  sleep 0.01;
  aws --region eu-west-1 batch deregister-job-definition --job-definition $x;
done

Containers​

Use rootless containers in Nextflow pipelines

Most containers use the root user by default. However, some users prefer to define a non-root user in the container to minimize the risk of privilege escalation. Because Nextflow and its tasks use a shared work directory to manage input and output data, using rootless containers can lead to file permissions errors in some environments:

touch: cannot touch '/fsx/work/ab/27d78d2b9b17ee895b88fcee794226/.command.begin': Permission denied

This should not occur when using AWS Batch from Seqera version 22.1.0. In other situations, you can avoid this issue by forcing all task containers to run as root. Add one of the following snippets to your Nextflow configuration:

// cloud executors
process.containerOptions = "--user 0:0"

// Kubernetes
k8s.securityContext = [
  "runAsUser": 0,
  "runAsGroup": 0
]

Git integration​

BitBucket authentication failure: Can't retrieve revisions for pipeline - https://my.bitbucketserver.com/path/to/pipeline/repo - Cause: Get branches operation not supported by BitbucketServerRepositoryProvider provider

If you supplied the correct BitBucket credentials and URL details in your tower.yml and still experience this error, update your version to at least v22.3.0. This version addresses SCM provider authentication issues and is likely to resolve the retrieval failure described here.

Optimization​

Optimized task failures: OutOfMemoryError: Container killed due to memory usage error

Improvements are being made to the way Nextflow calculates the optimal memory needed for containerized tasks, which will resolve issues with underestimating memory allocation in an upcoming release.

A temporary workaround for this issue is to implement a retry error strategy in the failing process that will increase the allocated memory each time the failed task is retried. Add the following errorStrategy block to the failing process:

process {
    errorStrategy = 'retry'
    maxRetries    = 3
    memory = { 1.GB * task.attempt }
}

Plugins​

Use the Nextflow SQL DB plugin to query AWS Athena

From Nextflow 22.05.0-edge, your Nextflow pipelines can query data from AWS Athena. Add these configuration items to your nextflow.config. The use of secrets is optional:

plugins {
  id 'nf-sqldb@0.4.0'
}

sql {
    db {
        'athena' {
              url = 'jdbc:awsathena://AwsRegion=YOUR_REGION;S3OutputLocation=s3://YOUR_S3_BUCKET'
              user = secrets.ATHENA_USER
              password = secrets.ATHENA_PASSWORD
            }
    }
}

Then, call the functionality in your workflow:

channel.sql.fromQuery("select * from test", db: "athena", emitColumns:true).view()
}

See here for more information.

Repositories​

Private Docker registry integration

Seqera-invoked jobs can pull container images from private Docker registries, such as JFrog Artifactory. The method to enable this depends on your computing platform.

For AWS Batch, modify your EC2 Launch Template using these AWS instructions.

note

This solution requires Docker Engine 17.07 or greater, to use --password-stdin.

You may need to add additional commands to your Launch template, depending on your security posture:
cp /root/.docker/config.json /home/ec2-user/.docker/config.json && chmod 777 /home/ec2-user/.docker/config.json

For Azure Batch, create a Container registry-type credential in your Seqera workspace and associate it with the Azure Batch compute environment defined in the same workspace.

For Kubernetes, use an imagePullSecret, per #2827.

Nextflow error: Remote resource not found

This error can occur if the Nextflow head job fails to retrieve the necessary repository credentials from Seqera. If your Nextflow log contains an entry like DEBUG nextflow.scm.RepositoryProvider - Request [credentials -:-], check the protocol of your instance's TOWER_SERVER_URL configuration value. This must be set to https rather than http (unless you are using TOWER_ENABLE_UNSAFE_MODE to allow HTTP connections to Seqera in a test environment).

Secrets​

Missing AWS execution role arn error during Seqera launch

The ECS Agent must have access to retrieve secrets from the AWS Secrets Manager. Secrets-using pipelines launched from your instance in an AWS Batch compute environment will encounter this error if an IAM Execution Role is not provided. See Secrets for more information.

AWS Batch task failures with secrets

You may encounter errors when executing pipelines that use secrets via AWS Batch:

  • If you use nf-sqldb version 0.4.1 or earlier and have secrets in your nextflow.config, you may encounter nextflow.secret.MissingSecretException: Unknown config secret errors in your Nextflow log. Resolve this error by explicitly defining the xpack-amzn plugin in your configuration:

    plugins {
      id 'xpack-amzn'
      id 'nf-sqldb'
    }

  • If you have two or more processes that use the same container image, but only a subset of these processes use secrets, your secret-using processes may fail during the initial run and then succeed when resumed. This is due to a bug in how Nextflow (22.07.1-edge and earlier) registers jobs with AWS Batch.

    To resolve the issue, upgrade your Nextflow to version 22.08.0-edge or later. If you cannot upgrade, use the following as workarounds:

    • Use a different container image for each process.
    • Define the same set of secrets in each process that uses the same container image.

Tower Agent​

"Unexpected Exception in WebSocket [...]: Operation timed out java.io.IOException: Operation timed out" error

We have improved Tower Agent reconnection logic with the release of version 0.5.0. Update your Tower Agent version before relaunching your pipeline.

Google​

VM preemption causes task interruptions

Running your pipelines on preemptible VMs provides significant cost savings, but increases the likelihood that a task will be interrupted before completion. It is a recommended best practice to implement a retry strategy when you encounter exit codes that are commonly related to preemption. For example:

process {
  errorStrategy = { task.exitStatus in [8,10,14] ? 'retry' : 'finish' }
  maxRetries    = 3
  maxErrors     = '-1'
}

Seqera Service account permissions for Google Life Sciences and GKE

The following roles must be granted to the nextflow-service-account:

  1. Cloud Life Sciences Workflows Runner
  2. Service Account User
  3. Service Usage Consumer
  4. Storage Object Admin

For detailed information, see this guide.

Kubernetes​

Invalid value: "xxx": must be less or equal to memory limit error

This error may be encountered when you specify a value in the Head Job memory field during the creation of a Kubernetes-type compute environment.

If you receive an error that includes field: spec.containers[x].resources.requests and message: Invalid value: "xxx": must be less than or equal to memory limit, your Kubernetes cluster may be configured with system resource limits which deny the Nextflow head job's resource request. To isolate the component causing the problem, try to launch a pod directly on your cluster via your Kubernetes administration solution. For example:

---
apiVersion: v1
kind: Pod
metadata:
  name: debug
  labels:
    app: debug
spec:
  containers:
    - name: debug
      image: busybox
      command: ["sh", "-c", "sleep 10"]
      resources:
        requests:
          memory: "xxxMi" # or "xxxGi"
  restartPolicy: Never

On-prem HPC​

java: command not found error

When submitting jobs to your on-prem HPC (using either SSH or Tower Agent authentication), the following error may appear in your Nextflow logs, even with Java on your PATH environment variable:

java: command not found
Nextflow is trying to use the Java VM defined for the following environment variables:
  JAVA_CMD: java
  NXF_OPTS:

Possible reasons for this error:

  1. The queue where the Nextflow head job runs is in a different environment/node than your login node userspace.
  2. If your HPC cluster uses modules, the Java module may not be loaded by default.

To troubleshoot:

  1. Open an interactive session with the head job queue.
  2. Launch the Nextflow job from the interactive session.
  3. If your cluster uses modules:
    • Add module load <your_java_module> in the Advanced Features > Pre-run script field when creating your HPC compute environment in Seqera.
  4. If your cluster doesn't use modules:
    1. Source an environment with Java and Nextflow using the Advanced Features > Pre-run script field when creating your HPC compute environment in Seqera.

Pipeline submissions to HPC clusters fail for some users

Nextflow launcher scripts will fail if processed by a non-Bash shell (e.g., zsh, tcsh). This problem can be identified from certain error entries:

  1. Your .nextflow.log contains an error like Invalid workflow status - expected: SUBMITTED; current: FAILED.
  2. Your Seqera Error report tab contains an error like:
Slurm job submission failed
- command: mkdir -p /home//\<USERNAME\>//scratch; cd /home//\<USERNAME\>//scratch; echo <LONG_BASE64_STRING> | base64 -d > nf-<RUN-ID>.launcher.sh; sbatch ./nf-<RUN-ID>.launcher.sh
- exit   : 1
- message: Submitted batch job <#>

Connect to the head node via SSH and run ps -p $$ to verify your default shell. If you see an entry other than Bash, fix as follows:

  1. Check which shells are available to you: cat /etc/shells
  2. Change your shell: chsh -s /usr/bin/bash (the path to the binary may differ, depending on your HPC configuration)
  3. If submissions continue to fail after this shell change, ask your Seqera Platform admin to restart the backend and cron containers, then submit again.