input/output error with cp symlink

[nal10]

I am working on a cloud computing platform and have data symlinked to a s3 bucket. I am trying to copy a zarr file (along with additional files) to another s3 location and am getting these errors for

    command = f"s5cmd run ../results/commands.txt"

    popen = subprocess.Popen(
        command, stdout=subprocess.PIPE, universal_newlines=True, shell=True
    )

ERROR "cp ../data/OMEZarr/image.zarr/0/0/0/10/76/5 s3://test_bucket/s5cmd_test/OMEZarr/image.zarr/0/0/0/10/76/5": BodyHashError: failed to compute body hashes caused by: read ../data/OMEZarr/image.zarr/0/0/0/10/76/5
ERROR "cp ../data/OMEZarr/image.zarr/0/0/0/32/37/33 s3://test_bucket/s5cmd_test/OMEZarr/image.zarr/0/0/0/32/37/33": open ../data/OMEZarr/image.zarr/0/0/0/32/37/33: input/output error

A single zarr can contain ~170,000 files and only a subset get these errors. I thought it may be bad symlinks, but if I run the same code again different files will have errors. Also, no error occur with awscli.

Thanks,
Nick