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google-deepmind / deepmind-research

This repository contains implementations and illustrative code to accompany DeepMind publications
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[enformer] enformer-training.ipynb failed to get dataset #300

Open zztin opened 2 years ago

zztin commented 2 years ago

Hi,

I am trying to run the notebooks provided by the author within the enformer package. However, I faced CA certification problem while running this line: human_dataset = get_dataset('human', 'train').batch(1).repeat()

The error message is FailedPreconditionError: Error executing an HTTP request: libcurl code 77 meaning 'Problem with the SSL CA cert (path? access rights?)', error details: error setting certificate verify locations: CAfile: /etc/ssl/certs/ca-certificates.crt CApath: none when reading metadata of gs://basenji_barnyard/data/human/statistics.json

Do you know how can I solve this?

zztin commented 2 years ago

Also for the section "Score variants in a VCF file" in the enformer-usage.ipynb, this line also fails with similar problem:

enformer_score_variants = EnformerScoreVariantsPCANormalized(model_path, transform_path, num_top_features=20)

The error message:

2021-11-12 14:28:55.158094: W tensorflow/core/platform/cloud/google_auth_provider.cc:184] All attempts to get a Google authentication bearer token failed, returning an empty token. Retrieving token from files failed with "Not found: Could not locate the credentials file.". Retrieving token from GCE failed with "Failed precondition: Error executing an HTTP request: libcurl code 6 meaning 'Couldn't resolve host name', error details: Couldn't resolve host 'metadata'".

FailedPreconditionError: Error executing an HTTP request: libcurl code 77 meaning 'Problem with the SSL CA cert (path? access rights?)', error details: error setting certificate verify locations: CAfile: /etc/ssl/certs/ca-certificates.crt CApath: none when reading gs://dm-enformer/models/enformer.finetuned.SAD.robustscaler-PCA500-robustscaler.transform.pkl

zztin commented 2 years ago

In short, To access files on gs://, I need some kind of certification. I do not have a SSL CAfile at this path: /etc/ssl/certs/ca-certificates.crt Do you know how I can create one that's valid?

HYsxe commented 2 years ago

Hey zztin,

I'm running into the same issue!

Kabongosalomon commented 2 years ago

Hi, is there any update on this issue ?

sheetalgiri commented 2 years ago

the issue appears to be one from tensorflow itself https://github.com/tensorflow/tensorflow/issues/40065