data/d10_1038_s41592_021_01344_8

[irena-starters]

Output

Run sfaira --help for an overview of all commands

Installed version v0.3.12+101.g7ca8c87b of sfaira is newer than the latest release 0.3.12! You are running a nightly version and features may break! Run sfaira upgrade to get the latest version. Running loader lint checks ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╺━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1 of 2 _validate_namespace Running loader lint checks ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╺━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1 of 2 _validate_namespace
Running yaml lint checks ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2 of 2 _validate_required_attributes

─────────────────────────────────────────────────────────────────────────────────────────────────────── LINT RESULTS ────────────────────────────────────────────────────────────────────────────────────────────────────────

 [[✔]]    3 tests passed
 [[!]]    0 tests had warnings
 [[✗]]    0 tests failed

───────────────────────────────────────────────────────────────────────────────────────────────────── [[✔]] Tests Passed ───────────────────────────────────────────────────────────────────────────────────────────────────── ╭────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮ │ Result: Passed required data loader load() namespace checks. │ │ Result: Passed required data loader section checks. │ │ Result: Passed required meta data checks. │ ╰────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯ Conflicts are not automatically resolved. In case of coflicts, please go back to https://www.ebi.ac.uk/ols/ontologies/cl and add the correct cell ontology class name into the .tsv "target" column. WARNING:nxontology.imports:Cannot add edge: MmusDv:0000000 --> MmusDv:0000038 (mouse life cycle stage --> infant stage): node does not exist in graph: MmusDv:0000038 WARNING:nxontology.imports:Cannot add edge: MmusDv:0000000 --> MmusDv:0000043 (mouse life cycle stage --> immature stage): node does not exist in graph: MmusDv:0000043 WARNING:nxontology.imports:Cannot add edge: MmusDv:0000000 --> MmusDv:0000044 (mouse life cycle stage --> 1-7 days): node does not exist in graph: MmusDv:0000044 WARNING:nxontology.imports:Cannot add edge: MmusDv:0000000 --> MmusDv:0000096 (mouse life cycle stage --> early immature stage): node does not exist in graph: MmusDv:0000096 /home/irena.sliskovic/.local/lib/python3.8/site-packages/anndata/_core/anndata.py:1785: FutureWarning: X.dtype being converted to np.float32 from float64. In the next version of anndata (0.9) conversion will not be automatic. Pass dtype explicitly to avoid this warning. Pass AnnData(X, dtype=X.dtype, ...) to get the future behavour. [AnnData(sparse.csr_matrix(a.shape), obs=a.obs) for a in all_adatas], transformed feature space on homosapiens_brain_2022_10x3v3_hezhisong_001_d10_1038_s41592_021_01344_8: log10 total counts 8.78 to 8.77, non-zero features 20248 to 19329 2023-03-02 09:15:05.733807: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libcudart.so.11.0'; dlerror: libcudart.so.11.0: cannot open shared object file: No such file or directory; LD_LIBRARY_PATH: /opt/R/lib/R/lib 2023-03-02 09:15:05.733842: I tensorflow/stream_executor/cuda/cudart_stub.cc:29] Ignore above cudart dlerror if you do not have a GPU set up on your machine. Completed testing of data loader, the data loader is now ready for use. Sfaira butler: "You data loader is finished!" "Proceed to phase 4 (publish) or use data loader." "Copy the following lines as a post into the pull request:"

Data loader test passed:

• homosapiens_brain_2022_10x3v3_hezhisong_001_d10_1038_s41592_021_01344_8