[BUG] Error opening output loom file

[Prathyusha-konda]

Hi, I finished grn -> ctx -> aucell analysis and have an output loom file which I am able to visualize on scope. But I am trying to combine this with my original seurat data for downstream analysis and I am unable to load the loom file due to the following errors. Can you please help me with how I can import this and if there is an alternative way to add this information to seurat object? Thank you very much!

> loom <- open_loom("output_pySCENIC_aucell.loom", mode = "r+")
Error in H5File.open(filename, mode, file_create_pl, file_access_pl) : 
  It is not possible to open the file. 
HDF5-API Errors:
    error #000: ../../src/hdf5-1.12.1/src/H5F.c in H5Fopen(): line 620: unable to open file
        class: HDF5
        major: File accessibility
        minor: Unable to open file

    error #001: ../../src/hdf5-1.12.1/src/H5VLcallback.c in H5VL_file_open(): line 3502: failed to iterate over available VOL connector plugins
        class: HDF5
        major: Virtual Object Layer
        minor: Iteration failed

    error #002: ../../src/hdf5-1.12.1/src/H5PLpath.c in H5PL__path_table_iterate(): line 579: can't iterate over plugins in plugin path '(null)'
        class: HDF5
        major: Plugin for dynamically loaded library
        minor: Iteration failed

    error #003: ../../src/hdf5-1.12.1/src/H5PLpath.c in H5PL__path_table_iterate_process_path(): line 620: can't open directory: /usr/local/hdf5/lib/plugin
        class: HDF5
        major: Plugin for dynamically loaded library
        minor: Can't open directory or fi

• pySCENIC version: [e.g. 0.10.0, use pyscenic -h at the command line]
  pyscenic==0.12.0+7.gc120979.dirty
• Installation method: Pip
• Run environment: Command line
• OS: Mac
• Package versions: [obtain using pip freeze, conda list, or skip this if using Docker/Singularity]:

aiohttp==3.8.3
aiosignal==1.2.0
anyio==3.6.2
appnope==0.1.3
arboreto==0.1.6
argon2-cffi==21.3.0
argon2-cffi-bindings==21.2.0
asttokens==2.1.0
async-timeout==4.0.2
attrs==22.1.0
Babel==2.11.0
backcall==0.2.0
beautifulsoup4==4.11.1
bleach==5.0.1
bokeh==2.4.3
boltons==21.0.0
certifi==2022.6.15
cffi==1.15.1
charset-normalizer==2.1.1
click==8.1.3
cloudpickle==2.2.0
contourpy==1.0.6
ctxcore==0.2.0
cycler==0.11.0
cytoolz==0.12.0
dask==2022.10.2
debugpy==1.6.3
decorator==5.1.1
defusedxml==0.7.1
dill==0.3.6
distributed==2022.10.2
entrypoints==0.4
executing==1.2.0
fastjsonschema==2.16.2
fonttools==4.38.0
frozendict==2.3.4
frozenlist==1.3.1
fsspec==2022.10.0
h5py==3.7.0
HeapDict==1.0.1
idna==3.4
interlap==0.2.7
ipykernel==6.17.0
ipython==8.6.0
ipython-genutils==0.2.0
jedi==0.18.1
Jinja2==3.1.2
joblib==1.2.0
json5==0.9.10
jsonschema==4.17.0
jupyter-server==1.21.0
jupyter_client==7.4.4
jupyter_core==4.11.2
jupyterlab==3.5.0
jupyterlab-pygments==0.2.2
jupyterlab_server==2.16.2
kiwisolver==1.4.4
llvmlite==0.39.1
locket==1.0.0
loompy==3.0.7
MarkupSafe==2.1.1
matplotlib==3.6.0
matplotlib-inline==0.1.6
mistune==2.0.4
msgpack==1.0.4
multidict==6.0.2
multiprocessing-on-dill==3.5.0a4
nbclassic==0.4.7
nbclient==0.7.0
nbconvert==7.2.3
nbformat==5.7.0
nest-asyncio==1.5.6
networkx==2.8.8
notebook==6.5.2
notebook_shim==0.2.0
numba==0.56.3
numexpr==2.8.4
numpy==1.23.4
numpy-groupies==0.9.20
packaging==21.3
pandas==1.5.1
pandocfilters==1.5.0
parso==0.8.3
partd==1.3.0
pexpect==4.8.0
pickleshare==0.7.5
Pillow==9.3.0
prometheus-client==0.15.0
prompt-toolkit==3.0.31
psutil==5.9.3
ptyprocess==0.7.0
pure-eval==0.2.2
pyarrow==10.0.0
pycparser==2.21
Pygments==2.13.0
pynndescent==0.5.8
pyparsing==3.0.9
pyrsistent==0.19.1
pyscenic==0.12.0+7.gc120979.dirty
python-dateutil==2.8.2
pytz==2022.6
PyYAML==6.0
pyzmq==24.0.1
requests==2.28.1
scikit-learn==1.1.3
scipy==1.9.3
seaborn==0.12.1
Send2Trash==1.8.0
six==1.16.0
sniffio==1.3.0
sortedcontainers==2.4.0
soupsieve==2.3.2.post1
stack-data==0.6.0
tblib==1.7.0
terminado==0.17.0
threadpoolctl==3.1.0
tinycss2==1.2.1
tomli==2.0.1
toolz==0.12.0
tornado==6.1
tqdm==4.64.1
traitlets==5.5.0
typing_extensions==4.4.0
umap-learn==0.5.3
urllib3==1.26.12
wcwidth==0.2.5
webencodings==0.5.1
websocket-client==1.4.1
yarl==1.8.1
zict==2.2.0

[SeppeDeWinter]

Hi @Prathyusha-konda

Sorry for the late reply.

Can you try opening the loom file like this:

lf = lp.connect( f_pyscenic_output, mode='r+', validate=False )

Hope this helps.

Best,

Seppe

[SebastianMHJohn]

Hi,
for me non of the above-mentioned suggestions worked out on a Mac M1, when I switched to a Windows computer I was able to follow mojaveazure/loomR#55.

Best wishes