Process `NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:FINALIZE:ADATA_TORDS (merged)` terminated with an error exit status
bug
### Description of the bug
I got an error when running test on my HPC.
### Command used and terminal output
```console
nextflow run nf-core/scdownstream \
-r dev \
-profile test,singularity,uppmax \
--project xxxxxxxxx \
-resume \
--outdir results \
-with-report report.html \
-with-timeline timeline.html \
-with-dag dag.png
```
```console
-[nf-core/scdownstream] Pipeline completed successfully, but with errored process(es) -
[1d/e035d1] NOTE: Process `NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:FINALIZE:ADATA_TORDS (merged)` terminated with an error exit status (1) -- Error is ignored
```
The full error from that python code:
```console
INFO: Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
INFO: Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred
INFO: Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
INFO: Environment variable SINGULARITYENV_SNIC_TMP is set, but APPTAINERENV_SNIC_TMP is preferred
Traceback (most recent call last):
File "/crex/proj/naiss2024-23-571/nobackup/roy/scdownstream/work/1d/e035d17b9a14f46856e3347b387c23/.command.sh", line 33, in <module>
adata = ad.read_h5ad("merged.h5ad")
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.12/site-packages/anndata/_io/h5ad.py", line 260, in read_h5ad
adata = read_dispatched(f, callback=callback)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.12/site-packages/anndata/experimental/_dispatch_io.py", line 42, in read_dispatched
return reader.read_elem(elem)
^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.12/site-packages/anndata/_io/utils.py", line 212, in func_wrapper
return func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.12/site-packages/anndata/_io/specs/registry.py", line 282, in read_elem
return self.callback(read_func, elem.name, elem, iospec=iospec)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.12/site-packages/anndata/_io/h5ad.py", line 244, in callback
k: read_dispatched(elem[k], callback)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.12/site-packages/anndata/experimental/_dispatch_io.py", line 42, in read_dispatched
return reader.read_elem(elem)
^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.12/site-packages/anndata/_io/utils.py", line 212, in func_wrapper
return func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.12/site-packages/anndata/_io/specs/registry.py", line 282, in read_elem
return self.callback(read_func, elem.name, elem, iospec=iospec)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.12/site-packages/anndata/_io/h5ad.py", line 258, in callback
return func(elem)
^^^^^^^^^^
File "/opt/conda/lib/python3.12/site-packages/anndata/_io/specs/methods.py", line 338, in read_mapping
return {k: _reader.read_elem(v) for k, v in elem.items()}
^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.12/site-packages/anndata/_io/utils.py", line 212, in func_wrapper
return func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.12/site-packages/anndata/_io/specs/registry.py", line 282, in read_elem
return self.callback(read_func, elem.name, elem, iospec=iospec)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.12/site-packages/anndata/_io/h5ad.py", line 258, in callback
return func(elem)
^^^^^^^^^^
File "/opt/conda/lib/python3.12/site-packages/anndata/_io/specs/methods.py", line 338, in read_mapping
return {k: _reader.read_elem(v) for k, v in elem.items()}
^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.12/site-packages/anndata/_io/utils.py", line 212, in func_wrapper
return func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.12/site-packages/anndata/_io/specs/registry.py", line 282, in read_elem
return self.callback(read_func, elem.name, elem, iospec=iospec)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.12/site-packages/anndata/_io/h5ad.py", line 258, in callback
return func(elem)
^^^^^^^^^^
File "/opt/conda/lib/python3.12/site-packages/anndata/_io/specs/methods.py", line 338, in read_mapping
return {k: _reader.read_elem(v) for k, v in elem.items()}
^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.12/site-packages/anndata/_io/utils.py", line 212, in func_wrapper
return func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.12/site-packages/anndata/_io/specs/registry.py", line 277, in read_elem
read_func: Read = self.registry.get_read(
^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.12/site-packages/anndata/_io/specs/registry.py", line 171, in get_read
raise IORegistryError._from_read_parts("read", self.read, src_type, spec)
anndata._io.specs.registry.IORegistryError: No read method registered for IOSpec(encoding_type='null', encoding_version='0.1.0') from <class 'h5py._hl.dataset.Dataset'>. You may need to update your installation of anndata.
Error raised while reading key 'layer' of <class 'h5py._hl.dataset.Dataset'> from /uns/bbknn-global-0.5_characteristic_genes/params
```
### Relevant files
[.nextflow.log](https://github.com/user-attachments/files/24642388/default.nextflow.log)
### System information
Nextflow: 25.10.2
nf-core: 3.5.1
Executor: slurm
Container engine: Apptainer
OS: CentOS Fedora Rocky Linux 9.7
nf-core/scdownstream: 0.0.1dev
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