MaximilianLombardo
commented
1 month ago Hi @HafsaKM thanks for reporting this. The automatic annotation feature is currently deprecated and not under active development. I've submitted a PR to remove this section of the documentation.
My code
Run the CELLxGENE annotate command
!cellxgene annotate adata_query.h5ad \ --model-url https://datasets.cellxgene.cziscience.com/8674c375-ae3a-433c-97de-3c56cf8f7304.h5ad\ --output-h5ad-file annotations/adata_query_annotated.h5ad \ --gene-column-name feature_name
Error output Reading query dataset adata_query.h5ad... Retrieving model from https://datasets.cellxgene.cziscience.com/8674c375-ae3a-433c-97de-3c56cf8f7304.h5ad Traceback (most recent call last): File "C:\Users\hafsa.conda\envs\sc_env\lib\runpy.py", line 197, in _run_module_as_main return _run_code(code, main_globals, None, File "C:\Users\hafsa.conda\envs\sc_env\lib\runpy.py", line 87, in _run_code exec(code, run_globals) File "C:\Users\hafsa.conda\envs\sc_env\Scripts\cellxgene.exe__main__.py", line 7, in
File "C:\Users\hafsa.conda\envs\sc_env\lib\site-packages\click\core.py", line 1157, in call
return self.main(args, kwargs)
File "C:\Users\hafsa.conda\envs\sc_env\lib\site-packages\click\core.py", line 1078, in main
rv = self.invoke(ctx)
File "C:\Users\hafsa.conda\envs\sc_env\lib\site-packages\click\core.py", line 1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "C:\Users\hafsa.conda\envs\sc_env\lib\site-packages\click\core.py", line 1434, in invoke
return ctx.invoke(self.callback, ctx.params)
File "C:\Users\hafsa.conda\envs\sc_env\lib\site-packages\click\core.py", line 783, in invoke
return __callback(args, **kwargs)
File "C:\Users\hafsa.conda\envs\sc_env\lib\site-packages\server\cli\annotate.py", line 166, in annotate
local_model_path = _retrieve_model(cli_args.get("model_cache_dir"), model_url, cli_args.get("use_model_cache"))
File "C:\Users\hafsa.conda\envs\sc_env\lib\site-packages\server\cli\annotate.py", line 224, in _retrieve_model
shutil.unpack_archive(model_archive_local_path, local_cache_model_path)
File "C:\Users\hafsa.conda\envs\sc_env\lib\shutil.py", line 1274, in unpack_archive
raise ReadError("Unknown archive format '{0}'".format(filename))
shutil.ReadError: Unknown archive format 'C:\Users\hafsa\AppData\Local\Temp\cellxgene_xfv0y7s5.h5ad'
Version (please complete the following information): cellxgene 1.2.0
Additional context I also tried downloading it locally and giving it the path to the zipped folder containing the h5ad file. But still gives me errors.