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How to Fix Common Issues

Logging into Docker / Synapse Docker Registry

During set up, entering docker login or docker login -u <synapse-username> docker.synapse.org returns the error message:

Authenticating with existing credentials...
Login did not succeed, error: Cannot connect to the Docker daemon at unix:///var/run/docker.sock. Is the docker daemon running?

Check to make sure that Docker app is turned on.

Logging into Synapse Docker Registry

During setup, entering docker login -u <synapse-username> docker.synapse.org returns the error message:

Error response from daemon: Get "https://docker.synapse.org/v2/": unauthorized: authentication required

Try logging out of Docker docker logout, logging back in docker login, and then reattempt Synapse Docker registry login docker login -u <synapse-username> docker.synapse.org

Creating CWL Job File

During data preprocessing, running bash RUN_model.sh <cancer> <platform> <method> <data> returns the error message:

Invalid input combination, see options in tools/options.yml

The combination (cancer, platform, method) you requested is not available. Classifiers are built with a specific set of statistical or data type assumptions - therefore some combinations are not allowed. Look in tools/options.yml for the allowed combinations - organized by method, cancer, and then by platform.

Running Machine Learning Models on Apple M1 Chip

When running Docker images, it returns the message and continues to run:

WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested

This automated message is to inform that the Docker image was built on a different platform, but will continue to run. This does not impact the analysis and will produce accurate results. Instead this message is meant to simply inform users.

Note: TensorFlow announced that TensorFlow 2.10 will support neural network machine learning models with Apple M1 chips. This means the deep learning method subSCOPE will run with TensorFlow 2.10+ on Apple M1 chips. If you are only able to run using an Apple M1, please make sure to check your version.