[BUG] The whole AUC matrix are 0 values

[baptisteavot-ukdri]

Exact same problem as described here: https://www.biostars.org/p/9577755/

The whole AUC matrix are 0s

 pyscenic grn --num_workers 25 expr_mat_1.tsv allTFs_hg38.txt --transpose -o expr_mat_1.adjacencies.tsv &> scenic.out

pyscenic ctx         expr_mat_1.adjacencies.tsv         hg19-tss-centered-5kb-7species.mc9nr.genes_vs_motifs.rankings.feather         hg19-tss-centered-10kb-7species.mc9nr.genes_vs_motifs.rankings.feather         --annotations_fname motifs-v9-nr.hgnc-m0.001-o0.0.tbl         --expression_mtx_fname expr_mat_1.tsv         --mode "custom_multiprocessing"         --output regulons.csv         --num_workers 15 --transpose --no_pruning --mask_dropouts

pyscenic aucell expr_mat_1.tsv regulons.csv         -o auc_mtx.csv         --num_workers 15 --auc_threshold 0.01

Everything runs fine without an error

I had to do some fixing of the code just like it is mentioned here, to avoid the warnings: #534

• pySCENIC version: 0.12.1
• Installed through PIP
• Run environment: CLI
• OS: Ubuntu 20.04.6 LTS
• Package versions:

aiohappyeyeballs==2.4.0
aiohttp==3.10.5
aiosignal==1.3.1
anyio==3.4.0
arboreto==0.1.6
argon2-cffi==21.2.0
argon2-cffi-bindings==21.2.0
async-timeout==4.0.3
attrs==19.3.0
Automat==0.8.0
Babel==2.9.1
backcall==0.2.0
bleach==4.1.0
blinker==1.4
boltons==24.0.0
certifi==2019.11.28
cffi==1.15.0
chardet==3.0.4
click==8.1.7
cloud-init==24.2
cloudpickle==3.0.0
colorama==0.4.3
command-not-found==0.3
configobj==5.0.6
constantly==15.1.0
contourpy==1.1.1
cryptography==2.8
ctxcore==0.2.0
cupshelpers==1.0
cycler==0.12.1
cytoolz==0.12.3
dask==2023.5.0
dbus-python==1.2.16
debugpy==1.5.1
decorator==5.1.0
defer==1.0.6
defusedxml==0.7.1
dill==0.3.8
distributed==2023.5.0
distro==1.4.0
distro-info==0.23+ubuntu1.1
entrypoints==0.3
fonttools==4.53.1
frozendict==2.4.4
frozenlist==1.4.1
fsspec==2024.9.0
h5py==3.11.0
httplib2==0.14.0
hyperlink==19.0.0
idna==2.8
importlib-metadata==8.5.0
importlib-resources==6.4.5
incremental==16.10.1
interlap==0.2.7
ipykernel==6.6.0
ipython==7.30.1
ipython-genutils==0.2.0
jedi==0.18.1
jinja2==3.1.4
joblib==1.4.2
json5==0.9.6
jsonpatch==1.22
jsonpointer==2.0
jsonschema==3.2.0
jupyter-client==7.1.0
jupyter-core==4.9.1
jupyter-server==1.13.0
jupyterlab==3.2.4
jupyterlab-pygments==0.1.2
jupyterlab-server==2.8.2
keyring==18.0.1
kiwisolver==1.4.7
language-selector==0.1
launchpadlib==1.10.13
lazr.restfulclient==0.14.2
lazr.uri==1.0.3
llvmlite==0.41.1
locket==1.0.0
loompy==3.0.7
lz4==4.3.3
macaroonbakery==1.3.1
MarkupSafe==2.1.5
matplotlib==3.7.5
matplotlib-inline==0.1.3
mistune==0.8.4
more-itertools==4.2.0
msgpack==1.1.0
multidict==6.1.0
multiprocessing-on-dill==3.5.0a4
nbclassic==0.3.4
nbclient==0.5.9
nbconvert==6.3.0
nbformat==5.1.3
nest-asyncio==1.5.4
netifaces==0.10.4
networkx==3.1
notebook==6.4.6
numba==0.58.1
numexpr==2.8.6
numpy==1.22.0
numpy-groupies==0.9.22
oauthlib==3.1.0
packaging==21.3
pandas==2.0.3
pandocfilters==1.5.0
parso==0.8.3
partd==1.4.1
pexpect==4.6.0
pickle5==0.0.11
pickleshare==0.7.5
pillow==10.4.0
prometheus-client==0.12.0
prompt-toolkit==3.0.23
protobuf==3.6.1
psutil==6.0.0
ptyprocess==0.7.0
pyarrow==17.0.0
pyasn1==0.4.2
pyasn1-modules==0.2.1
pycairo==1.16.2
pycparser==2.21
pycups==1.9.73
Pygments==2.10.0
PyGObject==3.36.0
PyHamcrest==1.9.0
PyJWT==1.7.1
pymacaroons==0.13.0
PyNaCl==1.3.0
pynndescent==0.5.13
pyOpenSSL==19.0.0
pyparsing==3.0.6
pyRFC3339==1.1
pyrsistent==0.15.5
pyscenic==0.12.1
pyserial==3.4
python-apt==2.0.1+ubuntu0.20.4.1
python-dateutil==2.8.2
python-debian==0.1.36+ubuntu1.1
pytz==2024.2
PyYAML==5.3.1
pyzmq==22.3.0
requests==2.22.0
requests-unixsocket==0.2.0
scikit-learn==1.3.2
scipy==1.7.3
seaborn==0.13.2
SecretStorage==2.3.1
Send2Trash==1.8.0
service-identity==18.1.0
simplejson==3.16.0
six==1.14.0
sniffio==1.2.0
sortedcontainers==2.4.0
sos==4.5.6
speedtest-cli==2.1.2
ssh-import-id==5.10
systemd-python==234
tblib==3.0.0
terminado==0.12.1
testpath==0.5.0
threadpoolctl==3.5.0
toolz==0.12.1
tornado==6.1
tqdm==4.66.5
traitlets==5.1.1
Twisted==18.9.0
typing-extensions==4.12.2
tzdata==2024.1
ubuntu-pro-client==8001
ufw==0.36
umap-learn==0.5.6
unattended-upgrades==0.1
urllib3==1.25.8
wadllib==1.3.3
wcwidth==0.2.5
webencodings==0.5.1
websocket-client==1.2.3
yarl==1.11.1
zict==3.0.0
zipp==3.20.2
zope.interface==4.7.1

[ghuls]

Make sure that all (most) of your gene names in your expression matrix are in HGNC gene symbols.

Use the following files for hg38:
hg38 motif to TF file: https://resources.aertslab.org/cistarget/motif2tf/motifs-v10nr_clust-nr.hgnc-m0.001-o0.0.tbl
hg38 motif gene database: https://resources.aertslab.org/cistarget/databases/homo_sapiens/hg38/refseq_r80/mc_v10_clust/gene_based/hg38_10kbp_up_10kbp_down_full_tx_v10_clust.genes_vs_motifs.rankings.feather
hg38 TF file: https://resources.aertslab.org/cistarget/tf_lists/allTFs_hg38.txt

[baptisteavot-ukdri]

It turned out I had to transpose the matrix, but thank you for the HG38 files, I could not find them initially