Need help with running pySCENIC ctx (step 6) using ENCODE track-base database

[nghiemdangvo]

Hi, thank you for the wonderful tool to develop SCENIC.

I am a new user and I am having some trouble trying to run the pySCENIC pipeline on CLI, while using the ENCODE track-base database instead of the motif ranking database as described in the standard workflow. This is just to refine the identified regulons that I have obtained with the previous standard workflow.

In detail, here are the details of my run (on local computer):

ChIP-seq databases obtained from the lab's website resource [https://resources.aertslab.org/cistarget/databases/homo_sapiens/hg38/refseq_r80/tc_v1]

encode_20190621__ChIP_seq_transcription_factor.hg38__refseq_r80-10kb_up_and_down_tss.max.genes_vs_tracks.rankings.feather

encode_20190621__ChIP_seq_transcription_factor.hg38__refseq-r80__10kb_up_and_down_tss.max.genes_vs_tracks.rankings.feather.sha1sum.txt

Here are the running command and following parameters:

pyscenic ctx ./data/adj.tsv \
> ./data/encode_20190621__ChIP_seq_transcription_factor.hg38__refseq-r80__10kb_up_and_down_tss.max.genes_vs_tracks.rankings.feather \
> --annotations_fname ./data/encode_20190621__ChIP_seq_transcription_factor.hg38__refseq-r80__10kb_up_and_down_tss.max.genes_vs_tracks.rankings.feather.sha1sum.txt \
> --expression_mtx_fname ./data/S9_preprocessed_SCENIC_input.loom \
> --mode "dask_multiprocessing" \
> --output reg_chip.csv --num_workers 4 --mask_dropouts

After running for a few minutes, the command terminated and thrown an error as follow:

Traceback (most recent call last):
File "/Users/DangVo/miniconda/envs/scrnaseq/bin/pyscenic", line 8, in
sys.exit(main())
File "/Users/DangVo/miniconda/envs/scrnaseq/lib/python3.9/site-packages/pyscenic/cli/pyscenic.py", line 677, in main
args.func(args)
File "/Users/DangVo/miniconda/envs/scrnaseq/lib/python3.9/site-packages/pyscenic/cli/pyscenic.py", line 221, in prune_targets_command
df_motifs = calc_func(
File "/Users/DangVo/miniconda/envs/scrnaseq/lib/python3.9/site-packages/pyscenic/prune.py", line 400, in prune2df
return _distributed_calc(
File "/Users/DangVo/miniconda/envs/scrnaseq/lib/python3.9/site-packages/pyscenic/prune.py", line 247, in _distributed_calc
motif_annotations = load_motif_annotations(
File "/Users/DangVo/miniconda/envs/scrnaseq/lib/python3.9/site-packages/pyscenic/utils.py", line 48, in load_motif_annotations
df = pd.read_csv(fname, sep='\t', index_col=[1, 0], usecols=column_names)
File "/Users/DangVo/miniconda/envs/scrnaseq/lib/python3.9/site-packages/pandas/util/_decorators.py", line 211, in wrapper
return func(*args, **kwargs)
File "/Users/DangVo/miniconda/envs/scrnaseq/lib/python3.9/site-packages/pandas/util/_decorators.py", line 317, in wrapper
return func(*args, **kwargs)
File "/Users/DangVo/miniconda/envs/scrnaseq/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 950, in read_csv
return _read(filepath_or_buffer, kwds)
File "/Users/DangVo/miniconda/envs/scrnaseq/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 605, in _read
parser = TextFileReader(filepath_or_buffer, **kwds)
File "/Users/DangVo/miniconda/envs/scrnaseq/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1442, in init
self._engine = self._make_engine(f, self.engine)
File "/Users/DangVo/miniconda/envs/scrnaseq/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1747, in _make_engine
return mapping[engine](f, **self.options)
File "/Users/DangVo/miniconda/envs/scrnaseq/lib/python3.9/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 148, in init
self._validate_usecols_names(usecols, self.orig_names)
File "/Users/DangVo/miniconda/envs/scrnaseq/lib/python3.9/site-packages/pandas/io/parsers/base_parser.py", line 918, in _validate_usecols_names
raise ValueError(
ValueError: Usecols do not match columns, columns expected but not found: ['description', '#motif_id', 'motif_similarity_qvalue', 'orthologous_identity', 'gene_name']

So my interpretation is that there is some mismatch in the formats of the expected data input, or could I have potentially not given the correct syntax for the pyscenic ctx command?

Computer configuration & software versions:
pySCENIC = 0.12.0 (run on conda env)
miniconda version = 4.14.0
python package versionconda list

Name Version Build Channel

adjusttext 0.7.3 pypi_0 pypi
aiohttp 3.8.3 pypi_0 pypi
aiosignal 1.2.0 pypi_0 pypi
alabaster 0.7.12 py_0 conda-forge
anndata 0.8.0 pyhd8ed1ab_1 conda-forge
aom 3.5.0 hf0c8a7f_0 conda-forge
appdirs 1.4.4 pyh9f0ad1d_0 conda-forge
applaunchservices 0.3.0 pyhd8ed1ab_2 conda-forge
appnope 0.1.3 pyhd8ed1ab_0 conda-forge
arboreto 0.1.6 pypi_0 pypi
argon2-cffi 21.3.0 pyhd8ed1ab_0 conda-forge
argon2-cffi-bindings 21.2.0 py39h63b48b0_2 conda-forge
arpack 3.7.0 hefb7bc6_2 conda-forge
arrow 1.2.3 pyhd8ed1ab_0 conda-forge
astroid 2.12.10 py39h6e9494a_0 conda-forge
async-timeout 4.0.2 pypi_0 pypi
atomicwrites 1.4.1 pyhd8ed1ab_0 conda-forge
attrs 22.1.0 pyh71513ae_1 conda-forge
autopep8 1.6.0 pyhd8ed1ab_1 conda-forge
babel 2.10.3 pyhd8ed1ab_0 conda-forge
backcall 0.2.0 pyh9f0ad1d_0 conda-forge
backports 1.0 py_2 conda-forge
backports.functools_lru_cache 1.6.4 pyhd8ed1ab_0 conda-forge
beautifulsoup4 4.11.1 pyha770c72_0 conda-forge
bedtools 2.30.0 h0e31d98_3 bioconda
binaryornot 0.4.4 py_1 conda-forge
biopython 1.79 py39h63b48b0_2 conda-forge
bioservices 1.10.0 pyhd8ed1ab_0 conda-forge
black 22.8.0 py39h6e9494a_0 conda-forge
bleach 5.0.1 pyhd8ed1ab_0 conda-forge
blosc 1.21.1 h97e831e_3 conda-forge
bokeh 2.4.3 pypi_0 pypi
boltons 21.0.0 pypi_0 pypi
brotli 1.0.9 h5eb16cf_7 conda-forge
brotli-bin 1.0.9 h5eb16cf_7 conda-forge
brotlipy 0.7.0 py39h63b48b0_1004 conda-forge
brunsli 0.1 h046ec9c_0 conda-forge
bzip2 1.0.8 h0d85af4_4 conda-forge
c-ares 1.18.1 h0d85af4_0 conda-forge
c-blosc2 2.4.2 had5f71b_0 conda-forge
ca-certificates 2022.9.24 h033912b_0 conda-forge
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
cellrank 1.5.1 pyhdfd78af_0 bioconda
certifi 2022.9.24 pyhd8ed1ab_0 conda-forge
cffi 1.15.1 py39hae9ecf2_0 conda-forge
cfitsio 4.1.0 h2c97ad1_0 conda-forge
chardet 5.0.0 py39h6e9494a_0 conda-forge
charls 2.3.4 he49afe7_0 conda-forge
charset-normalizer 2.1.1 pyhd8ed1ab_0 conda-forge
click 8.1.3 py39h6e9494a_0 conda-forge
cloudpickle 2.2.0 pyhd8ed1ab_0 conda-forge
colorama 0.4.5 pyhd8ed1ab_0 conda-forge
colorlog 6.7.0 py39h6e9494a_0 conda-forge
contourpy 1.0.5 py39h92daf61_0 conda-forge
cookiecutter 2.1.1 pyh6c4a22f_0 conda-forge
cryptography 37.0.1 py39hf6deb26_0
ctxcore 0.2.0 pypi_0 pypi
cycler 0.11.0 pyhd8ed1ab_0 conda-forge
cytoolz 0.12.0 py39h701faf5_0 conda-forge
dask-core 2022.9.2 pyhd8ed1ab_0 conda-forge
dav1d 1.0.0 hac89ed1_1 conda-forge
dbus 1.13.6 h811a1a6_3 conda-forge
debugpy 1.6.3 py39hd91caee_0 conda-forge
decorator 5.1.1 pyhd8ed1ab_0 conda-forge
defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge
diff-match-patch 20200713 pyh9f0ad1d_0 conda-forge
dill 0.3.5.1 pyhd8ed1ab_0 conda-forge
distributed 2022.9.2 pypi_0 pypi
docrep 0.3.2 pyh44b312d_0 conda-forge
docutils 0.19 py39h6e9494a_0 conda-forge
easydev 0.12.0 pyh6c4a22f_0 conda-forge
entrypoints 0.4 pyhd8ed1ab_0 conda-forge
expat 2.4.9 hf0c8a7f_0 conda-forge
fa2 0.3.5 py39h89e85a6_1 conda-forge
fftw 3.3.10 mpi_mpich_h4a8b384_5 conda-forge
flake8 4.0.1 pyhd8ed1ab_2 conda-forge
flit-core 3.7.1 pyhd8ed1ab_0 conda-forge
fonttools 4.37.4 py39ha30fb19_0 conda-forge
freetype 2.12.1 h3f81eb7_0 conda-forge
frozendict 2.3.4 pypi_0 pypi
frozenlist 1.3.1 pypi_0 pypi
fsspec 2022.8.2 pyhd8ed1ab_0 conda-forge
future 0.18.2 py39h6e9494a_5 conda-forge
gettext 0.19.8.1 hd1a6beb_1008 conda-forge
gevent 21.12.0 py39hf71ec93_2 conda-forge
giflib 5.2.1 hbcb3906_2 conda-forge
glpk 4.65 h0f52abe_1004 conda-forge
gmp 6.2.1 h2e338ed_0 conda-forge
greenlet 1.1.3 py39h7a8716b_0 conda-forge
grequests 0.6.0 pyh9f0ad1d_0 conda-forge
gseapy 0.13.0 py39h693c9d2_0 bioconda
h5py 3.7.0 nompi_py39hf4bc8c9_101 conda-forge
hdf5 1.12.2 mpi_mpich_hc154f39_0 conda-forge
heapdict 1.0.1 pypi_0 pypi
html5lib 1.1 pyh9f0ad1d_0 conda-forge
hypre 2.25.0 mpi_mpich_he15861c_0 conda-forge
icu 69.1 he49afe7_0 conda-forge
idna 3.4 pyhd8ed1ab_0 conda-forge
igraph 0.9.7 hacf96bb_0 conda-forge
imagecodecs 2022.9.26 py39h2af7347_0 conda-forge
imageio 2.22.0 pyhfa7a67d_0 conda-forge
imagesize 1.4.1 pyhd8ed1ab_0 conda-forge
importlib-metadata 4.11.4 py39h6e9494a_0 conda-forge
importlib_metadata 4.11.4 hd8ed1ab_0 conda-forge
importlib_resources 5.9.0 pyhd8ed1ab_0 conda-forge
inflection 0.5.1 pyh9f0ad1d_0 conda-forge
interlap 0.2.7 pypi_0 pypi
intervaltree 3.0.2 py_0 conda-forge
ipykernel 6.16.0 pyh736e0ef_0 conda-forge
ipython 7.33.0 py39h6e9494a_0 conda-forge
ipython_genutils 0.2.0 py_1 conda-forge
ipywidgets 8.0.2 pyhd8ed1ab_1 conda-forge
isort 5.10.1 pyhd8ed1ab_0 conda-forge
jaraco.classes 3.2.2 pyhd8ed1ab_0 conda-forge
jedi 0.18.1 pyhd8ed1ab_2 conda-forge
jellyfish 0.9.0 py39h63b48b0_1 conda-forge
jinja2 3.1.2 pyhd8ed1ab_1 conda-forge
jinja2-time 0.2.0 pyhd8ed1ab_3 conda-forge
joblib 1.2.0 pyhd8ed1ab_0 conda-forge
jpeg 9e hac89ed1_2 conda-forge
jsonschema 4.16.0 pyhd8ed1ab_0 conda-forge
jupyter_client 7.3.5 pyhd8ed1ab_0 conda-forge
jupyter_core 4.11.1 py39h6e9494a_0 conda-forge
jupyterlab_pygments 0.2.2 pyhd8ed1ab_0 conda-forge
jupyterlab_widgets 3.0.3 pyhd8ed1ab_0 conda-forge
jxrlib 1.1 h35c211d_2 conda-forge
keyring 23.9.3 py39h6e9494a_0 conda-forge
kiwisolver 1.4.4 py39h7c694c3_0 conda-forge
krb5 1.19.3 hb98e516_0 conda-forge
lazy-object-proxy 1.7.1 py39h63b48b0_1 conda-forge
lcms2 2.12 h577c468_0 conda-forge
leidenalg 0.8.9 py39hfd1d529_0 conda-forge
lerc 4.0.0 hb486fe8_0 conda-forge
libaec 1.0.6 he49afe7_0 conda-forge
libavif 0.10.1 he9a59b1_2 conda-forge
libblas 3.9.0 16_osx64_openblas conda-forge
libbrotlicommon 1.0.9 h5eb16cf_7 conda-forge
libbrotlidec 1.0.9 h5eb16cf_7 conda-forge
libbrotlienc 1.0.9 h5eb16cf_7 conda-forge
libcblas 3.9.0 16_osx64_openblas conda-forge
libclang 13.0.1 default_he082bbe_0 conda-forge
libcurl 7.85.0 h581aaea_0 conda-forge
libcxx 14.0.6 hccf4f1f_0 conda-forge
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libedit 3.1.20191231 h0678c8f_2 conda-forge
libev 4.33 haf1e3a3_1 conda-forge
libffi 3.4.2 h0d85af4_5 conda-forge
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libwebp-base 1.2.4 h775f41a_0 conda-forge
libxcb 1.13 h0d85af4_1004 conda-forge
libxml2 2.9.12 h7e28ab6_1 conda-forge
libxslt 1.1.33 h1acebb3_3 conda-forge
libzlib 1.2.12 hfd90126_4 conda-forge
libzopfli 1.0.3 h046ec9c_0 conda-forge
llvm-openmp 14.0.4 ha654fa7_0 conda-forge
llvmlite 0.39.1 py39had167e2_0 conda-forge
locket 1.0.0 pyhd8ed1ab_0 conda-forge
loompy 3.0.6 py_0 conda-forge
lxml 4.8.0 py39h63b48b0_2 conda-forge
lz4-c 1.9.3 he49afe7_1 conda-forge
markupsafe 2.1.1 py39h63b48b0_1 conda-forge
matplotlib-base 3.6.0 py39hb2f573b_0 conda-forge
matplotlib-inline 0.1.6 pyhd8ed1ab_0 conda-forge
mccabe 0.6.1 py_1 conda-forge
metis 5.1.0 h2e338ed_1006 conda-forge
mistune 2.0.4 pyhd8ed1ab_0 conda-forge
more-itertools 8.14.0 pyhd8ed1ab_0 conda-forge
mpfr 4.1.0 h0f52abe_1 conda-forge
mpi 1.0 mpich conda-forge
mpi4py 3.1.3 py39hef65b2c_2 conda-forge
mpich 4.0.2 hd33e60e_100 conda-forge
msgpack 1.0.4 pypi_0 pypi
multidict 6.0.2 pypi_0 pypi
multiprocessing-on-dill 3.5.0a4 pypi_0 pypi
mumps-include 5.2.1 h694c41f_11 conda-forge
mumps-mpi 5.2.1 h690e093_11 conda-forge
munkres 1.1.4 pyh9f0ad1d_0 conda-forge
mypy_extensions 0.4.3 py39h6e9494a_5 conda-forge
mysql-common 8.0.30 hc4b2c72_1 conda-forge
mysql-libs 8.0.30 h8658499_1 conda-forge
natsort 8.2.0 pyhd8ed1ab_0 conda-forge
nb_conda 2.2.1 py39h6e9494a_4 conda-forge
nb_conda_kernels 2.3.1 py39h6e9494a_1 conda-forge
nbclient 0.6.8 pyhd8ed1ab_0 conda-forge
nbconvert 7.1.0 pyhd8ed1ab_0 conda-forge
nbconvert-core 7.1.0 pyhd8ed1ab_0 conda-forge
nbconvert-pandoc 7.1.0 pyhd8ed1ab_0 conda-forge
nbformat 5.6.1 pyhd8ed1ab_0 conda-forge
ncls 0.0.65 py39h7222f55_1 bioconda
ncurses 6.3 h96cf925_1 conda-forge
nest-asyncio 1.5.6 pyhd8ed1ab_0 conda-forge
networkx 2.8.7 pyhd8ed1ab_0 conda-forge
notebook 6.4.12 pyha770c72_0 conda-forge
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numba 0.56.2 py39hf6b9d82_1 conda-forge
numexpr 2.8.3 pypi_0 pypi
numpy 1.23.3 py39h34843a6_0 conda-forge
numpy_groupies 0.9.19 pyhd8ed1ab_0 conda-forge
numpydoc 1.4.0 pyhd8ed1ab_1 conda-forge
openjpeg 2.5.0 h5d0d7b0_1 conda-forge
openssl 3.0.5 hfd90126_2 conda-forge
packaging 21.3 pyhd8ed1ab_0 conda-forge
pandas 1.5.0 py39hecff1ad_0 conda-forge
pandoc 2.19.2 h694c41f_0 conda-forge
pandocfilters 1.5.0 pyhd8ed1ab_0 conda-forge
parmetis 4.0.3 hb7fa8f8_1005 conda-forge
parso 0.8.3 pyhd8ed1ab_0 conda-forge
partd 1.3.0 pyhd8ed1ab_0 conda-forge
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pcre 8.45 he49afe7_0 conda-forge
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pexpect 4.8.0 pyh9f0ad1d_2 conda-forge
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pip 22.2.2 pyhd8ed1ab_0 conda-forge
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prometheus_client 0.14.1 pyhd8ed1ab_0 conda-forge
prompt-toolkit 3.0.31 pyha770c72_0 conda-forge
psutil 5.9.2 py39ha30fb19_0 conda-forge
pthread-stubs 0.4 hc929b4f_1001 conda-forge
ptscotch 6.0.9 h4f3afa6_2 conda-forge
ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge
pyarrow 9.0.0 pypi_0 pypi
pycodestyle 2.8.0 pyhd8ed1ab_0 conda-forge
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pydocstyle 6.1.1 pyhd8ed1ab_0 conda-forge
pyflakes 2.4.0 pyhd8ed1ab_0 conda-forge
pygam 0.8.0 py_0 conda-forge
pygments 2.13.0 pyhd8ed1ab_0 conda-forge
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pylint 2.15.3 pyhd8ed1ab_0 conda-forge
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pynndescent 0.5.7 pyh6c4a22f_0 conda-forge
pyobjc-core 8.5.1 py39h0504f80_0 conda-forge
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pyopenssl 22.0.0 pyhd8ed1ab_1 conda-forge
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pyqt 5.12.3 py39h6e9494a_8 conda-forge
pyqt-impl 5.12.3 py39he44290a_8 conda-forge
pyqt5-sip 4.19.18 py39h15fb055_8 conda-forge
pyqtchart 5.12 py39he44290a_8 conda-forge
pyqtwebengine 5.12.1 py39he44290a_8 conda-forge
pyranges 0.0.117 pyh5e36f6f_0 bioconda
pyrle 0.0.35 py39h7222f55_1 bioconda
pyroe 0.6.2 pyhdfd78af_0 bioconda
pyrsistent 0.18.1 py39h63b48b0_1 conda-forge
pyscenic 0.12.0 pypi_0 pypi
pysocks 1.7.1 pyha2e5f31_6 conda-forge
python 3.9.13 hf8d34f4_0_cpython conda-forge
python-annoy 1.17.0 py39hfd1d529_4 conda-forge
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python-fastjsonschema 2.16.2 pyhd8ed1ab_0 conda-forge
python-igraph 0.9.9 py39h8c2f370_0 conda-forge
python-lsp-black 1.2.1 pyhd8ed1ab_0 conda-forge
python-lsp-jsonrpc 1.0.0 pyhd8ed1ab_0 conda-forge
python-lsp-server 1.4.1 pyhd8ed1ab_1 conda-forge
python-slugify 6.1.2 pyhd8ed1ab_0 conda-forge
python-utils 3.3.3 pyhd8ed1ab_0 conda-forge
python.app 1.4 py39h89e85a6_0 conda-forge
python_abi 3.9 2_cp39 conda-forge
pytoolconfig 1.2.2 pyhd8ed1ab_0 conda-forge
pytz 2022.4 pyhd8ed1ab_0 conda-forge
pywavelets 1.3.0 py39h86b5767_1 conda-forge
pyyaml 6.0 py39h63b48b0_4 conda-forge
pyzmq 24.0.1 py39hed8f129_0 conda-forge
qdarkstyle 3.0.3 pyhd8ed1ab_0 conda-forge
qstylizer 0.2.2 pyhd8ed1ab_0 conda-forge
qt 5.12.9 h2a607e2_5 conda-forge
qtawesome 1.1.1 pyhd8ed1ab_0 conda-forge
qtconsole 5.3.2 pyhd8ed1ab_0 conda-forge
qtconsole-base 5.3.2 pyha770c72_0 conda-forge
qtpy 2.2.1 pyhd8ed1ab_0 conda-forge
readline 8.1.2 h3899abd_0 conda-forge
requests 2.28.1 pyhd8ed1ab_1 conda-forge
requests_cache 0.4.13 py_0 conda-forge
rope 1.3.0 pyhd8ed1ab_0 conda-forge
rtree 1.0.0 py39h7d0d40a_1 conda-forge
scalapack 2.2.0 hc746714_1 conda-forge
scanpy 1.9.1 pyhd8ed1ab_0 conda-forge
scikit-image 0.19.3 py39h0082581_1 conda-forge
scikit-learn 1.1.2 py39h8031a56_0 conda-forge
scipy 1.9.1 py39h9488793_0 conda-forge
scotch 6.0.9 h3da7401_2 conda-forge
scrublet 0.2.3 pyh5e36f6f_1 bioconda
scvelo 0.2.4 pyhdfd78af_0 bioconda
seaborn 0.12.0 hd8ed1ab_0 conda-forge
seaborn-base 0.12.0 pyhd8ed1ab_0 conda-forge
send2trash 1.8.0 pyhd8ed1ab_0 conda-forge
session-info 1.0.0 pyhd8ed1ab_0 conda-forge
setuptools 65.4.1 pyhd8ed1ab_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
slepc 3.17.2 real_hb732a19_100 conda-forge
slepc4py 3.17.2 real_h800f7ee_100 conda-forge
snappy 1.1.9 h6e38e02_1 conda-forge
snowballstemmer 2.2.0 pyhd8ed1ab_0 conda-forge
sorted_nearest 0.0.37 py39h7222f55_0 bioconda
sortedcontainers 2.4.0 pyhd8ed1ab_0 conda-forge
soupsieve 2.3.2.post1 pyhd8ed1ab_0 conda-forge
sphinx 5.2.3 pyhd8ed1ab_0 conda-forge
sphinxcontrib-applehelp 1.0.2 py_0 conda-forge
sphinxcontrib-devhelp 1.0.2 py_0 conda-forge
sphinxcontrib-htmlhelp 2.0.0 pyhd8ed1ab_0 conda-forge
sphinxcontrib-jsmath 1.0.1 py_0 conda-forge
sphinxcontrib-qthelp 1.0.3 py_0 conda-forge
sphinxcontrib-serializinghtml 1.1.5 pyhd8ed1ab_2 conda-forge
spyder 5.3.0 py39h6e9494a_0 conda-forge
spyder-kernels 2.3.3 py39h6e9494a_0 conda-forge
sqlite 3.39.4 h9ae0607_0 conda-forge
statsmodels 0.13.2 py39h15b18c7_0 conda-forge
stdlib-list 0.7.0 py_2 conda-forge
suds-community 1.1.2 pyhd8ed1ab_0 conda-forge
suitesparse 5.10.1 h7aff33d_1 conda-forge
superlu 5.2.2 h1f0f902_0 conda-forge
superlu_dist 7.2.0 h4bb6bf2_0 conda-forge
tabulate 0.8.10 pyhd8ed1ab_0 conda-forge
tbb 2021.6.0 hb8565cd_0 conda-forge
tblib 1.7.0 pypi_0 pypi
terminado 0.16.0 pyhd1c38e8_0 conda-forge
text-unidecode 1.3 py_0 conda-forge
textdistance 4.5.0 pyhd8ed1ab_0 conda-forge
texttable 1.6.4 pyhd8ed1ab_0 conda-forge
threadpoolctl 3.1.0 pyh8a188c0_0 conda-forge
three-merge 0.1.1 pyh9f0ad1d_0 conda-forge
tifffile 2022.8.12 pyhd8ed1ab_0 conda-forge
tinycss2 1.1.1 pyhd8ed1ab_0 conda-forge
tk 8.6.12 h5dbffcc_0 conda-forge
toml 0.10.2 pyhd8ed1ab_0 conda-forge
tomli 2.0.1 pyhd8ed1ab_0 conda-forge
tomlkit 0.11.5 pyha770c72_0 conda-forge
toolz 0.12.0 pyhd8ed1ab_0 conda-forge
tornado 6.2 py39h701faf5_0 conda-forge
tqdm 4.64.1 pyhd8ed1ab_0 conda-forge
traitlets 5.4.0 pyhd8ed1ab_0 conda-forge
typing 3.10.0.0 pyhd8ed1ab_0 conda-forge
typing-extensions 4.3.0 hd8ed1ab_0 conda-forge
typing_extensions 4.3.0 pyha770c72_0 conda-forge
tzdata 2022d h191b570_0 conda-forge
ujson 5.5.0 py39h7a8716b_0 conda-forge
umap-learn 0.5.3 py39h6e9494a_0 conda-forge
unicodedata2 14.0.0 py39h63b48b0_1 conda-forge
unidecode 1.3.6 pyhd8ed1ab_0 conda-forge
urllib3 1.26.11 pyhd8ed1ab_0 conda-forge
watchdog 2.1.9 py39h0056ad7_0 conda-forge
wcwidth 0.2.5 pyh9f0ad1d_2 conda-forge
webencodings 0.5.1 py_1 conda-forge
wheel 0.37.1 pyhd8ed1ab_0 conda-forge
widgetsnbextension 4.0.3 pyhd8ed1ab_0 conda-forge
wrapt 1.14.1 py39h701faf5_0 conda-forge
wurlitzer 3.0.2 pyhd8ed1ab_2 conda-forge
xmltodict 0.13.0 pyhd8ed1ab_0 conda-forge
xorg-libxau 1.0.9 h35c211d_0 conda-forge
xorg-libxdmcp 1.1.3 h35c211d_0 conda-forge
xz 5.2.6 h775f41a_0 conda-forge
yaml 0.2.5 h0d85af4_2 conda-forge
yapf 0.32.0 pyhd8ed1ab_0 conda-forge
yarl 1.8.1 pypi_0 pypi
zeromq 4.3.4 he49afe7_1 conda-forge
zfp 1.0.0 hb9aa9fd_1 conda-forge
zict 2.2.0 pypi_0 pypi
zipp 3.8.1 pyhd8ed1ab_0 conda-forge
zlib 1.2.12 hfd90126_4 conda-forge
zlib-ng 2.0.6 hac89ed1_0 conda-forge
zope.event 4.5.0 pyh9f0ad1d_0 conda-forge
zope.interface 5.4.0 py39h63b48b0_2 conda-forge
zstd 1.5.2 hfa58983_4 conda-forge

Any suggestion and support is really appreciated. Thanks so much in advance.

Best,

Dang

[Polligator]

not sure if this is right, you do understand that the data you are trying to use is for SCENIC+ not SCENIC, right?
also, I'm not sure if you can use .txt file as a database.

[nghiemdangvo]

Hi! thanks for your answer, I have too also figured out that I used the wrong ChIP track database for the code. I figured out to download the proper ChIP database and it worked. It's cool! 👍