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czbiohub-sf / tabula-muris

Code and annotations for the Tabula Muris single-cell transcriptomic dataset.
https://www.nature.com/articles/s41586-018-0590-4
BSD 3-Clause "New" or "Revised" License
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Unable to download .h5ad data #254

Open miguelreinacampos opened 8 months ago

miguelreinacampos commented 8 months ago

Hello,

I would like to access the .h5ad data files for analysis with python.

I tried downloading the .h5ad files from the AWS bucket, but these files are on GLACIER storage. I don't have the permission to initiate a retrieval process.

I followed the links mentioned here:

"You can download complete count files as sparse matrices using anndata's h5ad file format for use in Python here and here. You can process the resulting AnnData object using, for instance, Scanpy."

But, that both link to an error:

This XML file does not appear to have any style information associated with it. The document tree is shown below.

InvalidObjectState The operation is not valid for the object's storage class DEEP_ARCHIVE 35XDHRHT4AEQJWB8 ukU3SU4rWfcmR/skYBWH79JQ5g6QPeytgdozy9gPyF8PoyuQxlOc9qGAGUqHdkpWLOv2N5Wyu7A=

Thank you so much in advance for your help

Miguel Reina-Campos

aopisco commented 8 months ago

@miguelreinacampos this is indeed concerning. Can you try using the files from figshare instead? https://figshare.com/projects/Tabula_Muris_Senis/64982

Yanay1 commented 7 months ago

This error also occurs when trying to download the BAM files. It seems that they have been stored in DEEP_ARCHIVE so they cannot be downloaded.

14zac2 commented 7 months ago

I wanted to add that I am also unable to download anything off of AWS. I am getting "ERROR 403: Forbidden." when copying the AWS link and using wget, and an AccessDenied error when using the aws command-line tool.

kim-jzy123 commented 3 months ago

I wanted to add that I am also unable to download anything off of AWS. I am getting "ERROR 403: Forbidden." when copying the AWS link and using wget, and an AccessDenied error when using the aws command-line tool.

I got exactly the same error when using aws comman line tool in a Ubuntu system. With command 'aws s3 cp --no-sign-request "s3://czb-tabula-muris/TM_droplet_mat.rds" ./ --storage-class STANDARD --recursive --force-glacier-transfer' did not work either.