New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
error: Error -3 while decompressing data: invalid code lengths set #290
Comments
Hello, can you please share the full traceback? |
Hi I get the same error when using both Traceback:error Traceback (most recent call last) File /opt/conda/lib/python3.10/site-packages/decoupler/omnip.py:695, in translate_net(net, columns, source_organism, target_organism, id_type, unique_by, **kwargs) File /opt/conda/lib/python3.10/site-packages/pypath/utils/orthology.py:2262, in translate_df(df, target, source, cols, id_type, only_swissprot, oma, homologene, ensembl, oma_rel_type, oma_score, ensembl_hc, ensembl_types, **kwargs) File /opt/conda/lib/python3.10/site-packages/pypath/utils/orthology.py:620, in OrthologyManager.translate_df(self, df, target, source, cols, id_type, only_swissprot, oma, homologene, ensembl, oma_rel_type, oma_score, ensembl_hc, ensembl_types, **kwargs) File /opt/conda/lib/python3.10/site-packages/pypath/utils/orthology.py:515, in OrthologyManager.get_df(self, target, source, id_type, only_swissprot, oma, homologene, ensembl, oma_rel_type, oma_score, ensembl_hc, ensembl_types, full_records, **kwargs) File /opt/conda/lib/python3.10/site-packages/pypath/utils/orthology.py:233, in OrthologyManager.which_table(self, target, source, only_swissprot, resource, id_type) File /opt/conda/lib/python3.10/site-packages/pypath/utils/orthology.py:242, in OrthologyManager.load(self, key) File /opt/conda/lib/python3.10/site-packages/pypath/utils/orthology.py:1492, in OmaOrthology.init(self, target, source, id_type, only_swissprot, rel_type, score) File /opt/conda/lib/python3.10/site-packages/pypath/utils/orthology.py:869, in ProteinOrthology.init(self, target, source, id_type, only_swissprot, **kwargs) File /opt/conda/lib/python3.10/site-packages/pypath/utils/orthology.py:1506, in OmaOrthology.load(self) File /opt/conda/lib/python3.10/site-packages/pypath/inputs/oma.py:125, in oma_orthologs(organism_a, organism_b, id_type, rel_type, score, return_df) File /opt/conda/lib/python3.10/site-packages/pypath/inputs/oma.py:139, in (.0) File /opt/conda/lib/python3.10/site-packages/pypath/inputs/oma.py:244, in id_translate(id, taxon, id_type) File /opt/conda/lib/python3.10/site-packages/pypath/utils/mapping.py:3551, in map_name(name, id_type, target_id_type, ncbi_tax_id, strict, expand_complexes, uniprot_cleanup) File /opt/conda/lib/python3.10/site-packages/pypath_common/_misc.py:2935, in ignore_unhashable..wrapper(*args, **kwargs) File /opt/conda/lib/python3.10/site-packages/pypath/utils/mapping.py:2193, in Mapper.map_name(self, name, id_type, target_id_type, ncbi_tax_id, strict, expand_complexes, uniprot_cleanup) File /opt/conda/lib/python3.10/site-packages/pypath/utils/mapping.py:2227, in Mapper.uniprot_cleanup(self, uniprots, ncbi_tax_id) File /opt/conda/lib/python3.10/site-packages/pypath/utils/mapping.py:2868, in Mapper.trembl_swissprot(self, uniprots, ncbi_tax_id) File /opt/conda/lib/python3.10/site-packages/pypath_common/_misc.py:2935, in ignore_unhashable..wrapper(*args, **kwargs) File /opt/conda/lib/python3.10/site-packages/pypath/utils/mapping.py:1978, in Mapper.map_name(self, name, id_type, target_id_type, ncbi_tax_id, strict, expand_complexes, uniprot_cleanup) File /opt/conda/lib/python3.10/site-packages/pypath/utils/mapping.py:2510, in Mapper._map_name(self, name, id_type, target_id_type, ncbi_tax_id) File /opt/conda/lib/python3.10/site-packages/pypath/utils/mapping.py:1562, in Mapper.which_table(self, id_type, target_id_type, load, ncbi_tax_id) File /opt/conda/lib/python3.10/site-packages/pypath/utils/mapping.py:3208, in Mapper.load_mapping(self, resource, **kwargs) File /opt/conda/lib/python3.10/site-packages/pypath/utils/mapping.py:258, in MapReader.init(self, param, ncbi_tax_id, entity_type, load_a_to_b, load_b_to_a, uniprots, lifetime, resource_id_types) File /opt/conda/lib/python3.10/site-packages/pypath/utils/mapping.py:288, in MapReader.load(self) File /opt/conda/lib/python3.10/site-packages/pypath/utils/mapping.py:450, in MapReader.read(self) File /opt/conda/lib/python3.10/site-packages/pypath/utils/mapping.py:893, in MapReader.read_mapping_uniprot(self) File /opt/conda/lib/python3.10/site-packages/pypath/inputs/uniprot.py:681, in UniprotQuery.perform(self) File /opt/conda/lib/python3.10/site-packages/pypath/inputs/uniprot.py:656, in UniprotQuery.iter(self) File /opt/conda/lib/python3.10/site-packages/pypath/share/curl.py:766, in FileOpener.iterfile(fileobj) File /opt/conda/lib/python3.10/gzip.py:314, in GzipFile.read1(self, size) File /opt/conda/lib/python3.10/_compression.py:68, in DecompressReader.readinto(self, b) File /opt/conda/lib/python3.10/gzip.py:496, in _GzipReader.read(self, size) error: Error -3 while decompressing data: invalid block type python version: 3.10 absl-py 1.4.0 |
Dear developer,
I get an error when running the following code:
progeny = dc.get_progeny(organism='Mus musculus', top=500)
the error is : error: Error -3 while decompressing data: invalid code lengths set
Desktop (please complete the following information):
-package version:
absl-py 1.4.0
aiohttp 3.8.3
aiosignal 1.3.1
alembic 1.9.1
anndata 0.8.0
annotated-types 0.6.0
annoy 1.17.1
anyio 3.6.2
appdirs 1.4.4
argon2-cffi 21.3.0
argon2-cffi-bindings 21.2.0
asttokens 2.2.1
async-generator 1.10
async-timeout 4.0.2
attrs 22.2.0
Babel 2.11.0
backcall 0.2.0
backports.functools-lru-cache 1.6.4
bcrypt 4.1.2
beautifulsoup4 4.11.1
bleach 6.0.0
blinker 1.5
bokeh 3.0.3
boltons 23.1.1
Bottleneck 1.3.6
brotlipy 0.7.0
cached-property 1.5.2
cachetools 5.3.0
cell2location 0.1.3
certifi 2024.2.2
certipy 0.1.3
cffi 1.15.1
charset-normalizer 2.1.1
chex 0.1.7
click 8.1.3
cloudpickle 2.2.1
cmake 3.26.1
colorama 0.4.6
comm 0.1.2
conda 22.11.1
conda-package-handling 2.0.2
conda_package_streaming 0.7.0
contextlib2 21.6.0
contourpy 1.0.7
cryptography 42.0.5
cycler 0.11.0
Cython 0.29.33
cytoolz 0.12.0
dask 2022.11.0
debugpy 1.6.6
decorator 5.1.1
decoupler 1.6.0
defusedxml 0.7.1
detecto 1.2.2
dill 0.3.6
distributed 2022.11.0
dm-tree 0.1.8
docrep 0.3.2
entrypoints 0.4
et-xmlfile 1.1.0
etils 1.2.0
exceptiongroup 1.1.1
executing 1.2.0
face 20.1.1
fastjsonschema 2.16.2
flax 0.6.8
flit_core 3.8.0
fonttools 4.38.0
frozenlist 1.3.3
fsspec 2023.1.0
future 0.18.3
glom 23.5.0
gmpy2 2.1.2
google-auth 2.16.0
google-auth-oauthlib 0.4.6
greenlet 2.0.2
grpcio 1.51.1
h5py 3.8.0
HeapDict 1.0.1
hyperopt 0.2.7
idna 3.4
igraph 0.10.3
imagecodecs 2023.1.23
imageio 2.25.0
importlib-metadata 6.0.0
importlib-resources 5.10.2
inflect 7.0.0
iniconfig 2.0.0
ipykernel 6.21.0
ipympl 0.9.2
ipython 8.12.0
ipython-genutils 0.2.0
ipywidgets 8.0.4
jax 0.4.8
jaxlib 0.4.7
jedi 0.18.2
Jinja2 3.1.2
joblib 1.2.0
json5 0.9.5
jsonschema 4.17.3
jupyter-client 7.3.4
jupyter_core 5.2.0
jupyter-events 0.6.3
jupyter-server 1.23.5
jupyter_server_terminals 0.4.4
jupyter-starters 1.1.0
jupyter-telemetry 0.1.0
jupyterhub 3.1.1
jupyterlab 3.5.3
jupyterlab-pygments 0.2.2
jupyterlab_server 2.19.0
jupyterlab-widgets 3.0.5
kiwisolver 1.4.4
leidenalg 0.9.1
libmambapy 1.2.0
lightning-utilities 0.8.0
lit 16.0.0
llvmlite 0.39.1
locket 1.0.0
loompy 3.0.6
louvain 0.8.0
lxml 5.1.0
lz4 4.2.0
Mako 1.2.4
mamba 1.2.0
Markdown 3.4.1
markdown-it-py 2.2.0
MarkupSafe 2.1.2
matplotlib 3.7.1
matplotlib-inline 0.1.6
mdurl 0.1.2
mistune 2.0.4
ml-collections 0.1.1
ml-dtypes 0.0.4
mpmath 1.3.0
msgpack 1.0.5
mudata 0.2.1
multidict 6.0.4
multipledispatch 0.6.0
munkres 1.1.4
natsort 8.3.1
nbclassic 0.4.8
nbclient 0.7.2
nbconvert 7.2.9
nbformat 5.7.3
nbresuse 0.4.0
nest-asyncio 1.5.6
networkx 3.0
nose 1.3.7
notebook 6.5.2
notebook_shim 0.2.2
numba 0.56.4
numexpr 2.7.3
numpy 1.23.5
numpy-groupies 0.9.20
numpyro 0.11.0
nvidia-cuda-cupti-cu11 11.7.101
nvidia-cuda-nvrtc-cu11 11.7.99
nvidia-cuda-runtime-cu11 11.7.99
nvidia-cufft-cu11 10.9.0.58
nvidia-curand-cu11 10.2.10.91
nvidia-cusparse-cu11 11.7.4.91
nvidia-nccl-cu11 2.14.3
nvidia-nvtx-cu11 11.7.91
oauthlib 3.2.2
omnipath 1.0.8
opencv-python 4.7.0
openpyxl 3.1.2
opt-einsum 3.3.0
optax 0.1.4
orbax 0.1.7
packaging 23.0
pamela 1.0.0
pandas 2.0.0
pandocfilters 1.5.0
paramiko 3.4.0
parso 0.8.3
partd 1.3.0
patsy 0.5.3
pexpect 4.8.0
pickleshare 0.7.5
Pillow 9.4.0
pip 23.0.1
pkgutil_resolve_name 1.3.10
platformdirs 2.6.2
plotly 5.14.1
pluggy 1.0.0
ply 3.11
pooch 1.6.0
prometheus-client 0.16.0
prompt-toolkit 3.0.36
protobuf 4.21.12
psutil 5.9.4
ptyprocess 0.7.0
pure-eval 0.2.2
py4j 0.10.9.7
pyasn1 0.4.8
pyasn1-modules 0.2.7
pycosat 0.6.4
pycparser 2.21
pycurl 7.45.1
pydantic 2.6.4
pydantic_core 2.16.3
pygeos 0.14
Pygments 2.14.0
PyJWT 2.6.0
PyNaCl 1.5.0
pynndescent 0.5.8
pyOpenSSL 23.0.0
pyparsing 3.0.9
pypath_common 0.2.0
pypath-omnipath 0.16.10
PyQt5 5.15.7
PyQt5-sip 12.11.0
pyreadr 0.5.0
pyro-api 0.1.2
pyro-ppl 1.8.4
pyrsistent 0.19.3
pysftp 0.2.9
PySocks 1.7.1
pytest 7.2.2
python-dateutil 2.8.2
python-json-logger 2.0.4
python-louvain 0.16
pytorch-lightning 1.9.4
pytz 2022.7.1
pyu2f 0.1.5
PyWavelets 1.4.1
PyYAML 6.0
pyzmq 25.0.0
rdata 0.11.2
requests 2.28.2
requests-oauthlib 1.3.1
rfc3339-validator 0.1.4
rfc3986-validator 0.1.1
rich 13.3.3
rsa 4.9
ruamel.yaml 0.17.21
ruamel.yaml.clib 0.2.7
scanpy 1.9.3
scikit-image 0.19.3
scikit-learn 1.2.1
scipy 1.10.1
scvi-tools 0.20.3
seaborn 0.12.2
Send2Trash 1.8.0
session-info 1.0.0
setuptools 66.1.1
shapely 2.0.1
sip 6.7.7
six 1.16.0
sniffio 1.3.0
snuggs 1.4.7
sortedcontainers 2.4.0
soupsieve 2.3.2.post1
SQLAlchemy 2.0.0
sqlparse 0.4.4
stack-data 0.6.2
statsmodels 0.13.5
stdlib-list 0.8.0
sympy 1.11.1
tables 3.7.0
tabulate 0.9.0
tblib 1.7.0
tensorboard 2.11.2
tensorboard-data-server 0.6.1
tensorboard-plugin-wit 1.8.1
tensorstore 0.1.35
terminado 0.17.1
texttable 1.6.7
threadpoolctl 3.1.0
tifffile 2023.1.23.1
timeloop 1.0.2
tinycss2 1.2.1
toml 0.10.2
tomli 2.0.1
toolz 0.12.0
torch 1.13.1
torchaudio 0.13.1
torchmetrics 0.11.4
torchvision 0.14.1
tornado 6.1
tqdm 4.64.1
traitlets 5.9.0
typing_extensions 4.10.0
tzdata 2023.3
umap-learn 0.5.3
unicodedata2 15.0.0
urllib3 1.26.14
vincent 0.4.4
wcwidth 0.2.6
webencodings 0.5.1
websocket-client 1.5.0
Werkzeug 2.2.2
wheel 0.38.4
widgetsnbextension 4.0.5
wrapt 1.16.0
xarray 2024.2.0
xlrd 2.0.1
xyzservices 2022.9.0
yarl 1.8.2
zict 2.2.0
zipp 3.12.0
zstandard 0.19.0
The text was updated successfully, but these errors were encountered: