pySCENIC
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Published
20 hours ago •
aertslab
aertslab
pyarrow.lib.ArrowInvalid: Not a feather file
I am currently using pyscenic ctx for analysis, but I encountered the following error:
Traceback (most recent call last):
File "/home/qiruicheng/anaconda3/envs/scenic_protocol/bin/pyscenic", line 8, in <module>
sys.exit(main())
File "/home/qiruicheng/anaconda3/envs/scenic_protocol/lib/python3.6/site-packages/pyscenic/cli/pyscenic.py", line 675, in main
args.func(args)
File "/home/qiruicheng/anaconda3/envs/scenic_protocol/lib/python3.6/site-packages/pyscenic/cli/pyscenic.py", line 230, in prune_targets_command
num_workers=args.num_workers,
File "/home/qiruicheng/anaconda3/envs/scenic_protocol/lib/python3.6/site-packages/pyscenic/prune.py", line 410, in prune2df
module_chunksize,
File "/home/qiruicheng/anaconda3/envs/scenic_protocol/lib/python3.6/site-packages/pyscenic/prune.py", line 334, in _distributed_calc
scheduler='processes', num_workers=num_workers if num_workers else cpu_count()
File "/home/qiruicheng/anaconda3/envs/scenic_protocol/lib/python3.6/site-packages/dask/base.py", line 283, in compute
(result,) = compute(self, traverse=False, **kwargs)
File "/home/qiruicheng/anaconda3/envs/scenic_protocol/lib/python3.6/site-packages/dask/base.py", line 565, in compute
results = schedule(dsk, keys, **kwargs)
File "/home/qiruicheng/anaconda3/envs/scenic_protocol/lib/python3.6/site-packages/dask/multiprocessing.py", line 230, in get
**kwargs
File "/home/qiruicheng/anaconda3/envs/scenic_protocol/lib/python3.6/site-packages/dask/local.py", line 487, in get_async
raise_exception(exc, tb)
File "/home/qiruicheng/anaconda3/envs/scenic_protocol/lib/python3.6/site-packages/dask/local.py", line 316, in reraise
raise exc.with_traceback(tb)
File "/home/qiruicheng/anaconda3/envs/scenic_protocol/lib/python3.6/site-packages/dask/local.py", line 222, in execute_task
result = _execute_task(task, data)
File "/home/qiruicheng/anaconda3/envs/scenic_protocol/lib/python3.6/site-packages/dask/core.py", line 121, in _execute_task
return func(*(_execute_task(a, cache) for a in args))
File "/home/qiruicheng/anaconda3/envs/scenic_protocol/lib/python3.6/site-packages/dask/core.py", line 121, in <genexpr>
return func(*(_execute_task(a, cache) for a in args))
File "/home/qiruicheng/anaconda3/envs/scenic_protocol/lib/python3.6/site-packages/dask/core.py", line 121, in _execute_task
return func(*(_execute_task(a, cache) for a in args))
File "/home/qiruicheng/anaconda3/envs/scenic_protocol/lib/python3.6/site-packages/pyscenic/transform.py", line 301, in modules2df
[module2df(db, module, motif_annotations, weighted_recovery, False, module2features_func) for module in modules]
File "/home/qiruicheng/anaconda3/envs/scenic_protocol/lib/python3.6/site-packages/pyscenic/transform.py", line 301, in <listcomp>
[module2df(db, module, motif_annotations, weighted_recovery, False, module2features_func) for module in modules]
File "/home/qiruicheng/anaconda3/envs/scenic_protocol/lib/python3.6/site-packages/pyscenic/transform.py", line 231, in module2df
db, module, motif_annotations, weighted_recovery=weighted_recovery
File "/home/qiruicheng/anaconda3/envs/scenic_protocol/lib/python3.6/site-packages/pyscenic/transform.py", line 152, in module2features_auc1st_impl
df = db.load(module)
File "/home/qiruicheng/anaconda3/envs/scenic_protocol/lib/python3.6/site-packages/ctxcore/rnkdb.py", line 318, in load
gene_set = self.geneset.intersection(set(gs.genes))
File "cytoolz/functoolz.pyx", line 475, in cytoolz.functoolz._memoize.__call__
File "/home/qiruicheng/anaconda3/envs/scenic_protocol/lib/python3.6/site-packages/ctxcore/rnkdb.py", line 98, in geneset
return set(self.genes)
File "cytoolz/functoolz.pyx", line 475, in cytoolz.functoolz._memoize.__call__
File "/home/qiruicheng/anaconda3/envs/scenic_protocol/lib/python3.6/site-packages/ctxcore/rnkdb.py", line 296, in genes
reader = FeatherReader(self._fname)
File "/home/qiruicheng/anaconda3/envs/scenic_protocol/lib/python3.6/site-packages/pyarrow/feather.py", line 40, in __init__
self.open(source)
File "pyarrow/feather.pxi", line 83, in pyarrow.lib.FeatherReader.open
File "pyarrow/error.pxi", line 84, in pyarrow.lib.check_status
pyarrow.lib.ArrowInvalid: Not a feather file
Command run when the error occurred:
f_loom_path_scenic=outputs/${sn}.loom
## outputs
grn_output=outputs/${sn}.adj.tsv
ctx_output=outputs_new/${sn}.reg.tsv
f_pyscenic_output=outputs_new/${sn}.pyscenic.loom
## reference
f_tfs=../cisTarget_databases/allTFs_mm.txt
# f_motif_path=../cisTarget_databases/motifs-v9-nr.mgi-m0.001-o0.0.tbl
# f_db_names=../cisTarget_databases/old_version/mm9-tss-centered-10kb-7species.mc9nr.feather
f_motif_path=../cisTarget_databases/motifs-v10nr_clust-nr.mgi-m0.001-o0.0.tbl
f_db_names=`find ../cisTarget_databases/ -name "mm10*10kbp*rankings.feather"`
#arboreto_with_multiprocessing.py \
# $f_loom_path_scenic \
# $f_tfs \
# --method grnboost2 \
# --output $grn_output \
# --num_workers 20 \
# --seed 777
pyscenic ctx \
$grn_output \
$f_db_names \
--annotations_fname $f_motif_path \
--expression_mtx_fname $f_loom_path_scenic \
--output $ctx_output \
--num_workers 10
I suspect that the issue may be with my feather file. I have tried downloading both the mm10 v10 versions of the feather files using the following links: (https://resources.aertslab.org/cistarget/databases/mus_musculus/mm10/refseq_r80/mc_v10_clust/gene_based/mm10_10kbp_up_10kbp_down_full_tx_v10_clust.genes_vs_motifs.rankings.feather)
However, even when I tried using the v9 version of the feather file, I still encountered the same error. (https://resources.aertslab.org/cistarget/databases/mus_musculus/mm10/refseq_r80/mc9nr/gene_based/mm10__refseq-r80__10kb_up_and_down_tss.mc9nr.genes_vs_motifs.rankings.feather)
It is worth noting that when I used the previous mm9 version of the feather file, the program was able to run without any issues. (I used mm10 as a reference genome) Does this mean that I made a mistake while processing the mm10 version of the feather file? If anyone has any suggestions to help me solve this issue, please leave a comment below. Thank you!
Expected behavior A clear and concise description of what you expected to happen.
Please complete the following information:
- pySCENIC version: 0.11.2
- Installation method: anaconda
- Run environment: CLI
- OS: CentOS7
- Package versions:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
_openmp_mutex 4.5 2_gnu https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
_r-mutex 1.0.1 anacondar_1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
aiohttp 3.8.4 pypi_0 pypi
aiosignal 1.2.0 pypi_0 pypi
arboreto 0.1.6 pypi_0 pypi
async-timeout 4.0.2 pypi_0 pypi
asynctest 0.13.0 pypi_0 pypi
attrs 22.2.0 pypi_0 pypi
aws-c-auth 0.6.21 h774e2f3_1 conda-forge
aws-c-cal 0.5.20 hd3b2fe5_3 conda-forge
aws-c-common 0.8.5 h166bdaf_0 conda-forge
aws-c-compression 0.2.16 hf5f93bc_0 conda-forge
aws-c-event-stream 0.2.16 h52dae97_0 conda-forge
aws-c-http 0.6.29 hf21410f_0 conda-forge
aws-c-io 0.13.11 h4f448d1_2 conda-forge
aws-c-mqtt 0.7.13 hefb3e95_10 conda-forge
aws-c-s3 0.2.1 h2b8044a_2 conda-forge
aws-c-sdkutils 0.1.7 hf5f93bc_0 conda-forge
aws-checksums 0.1.14 h6027aba_0 conda-forge
aws-crt-cpp 0.18.16 h89864ff_5 conda-forge
aws-sdk-cpp 1.9.379 hc894300_6 conda-forge
binutils_impl_linux-64 2.39 h6ceecb4_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
bioconductor-annotate 1.72.0 r41hdfd78af_0 bioconda
bioconductor-annotationdbi 1.56.2 r41hdfd78af_0 bioconda
bioconductor-aucell 1.16.0 r41hdfd78af_0 bioconda
bioconductor-biobase 2.54.0 r41hc0cfd56_2 bioconda
bioconductor-biocgenerics 0.40.0 r41hdfd78af_0 bioconda
bioconductor-biostrings 2.62.0 r41hc0cfd56_2 bioconda
bioconductor-delayedarray 0.20.0 r41hc0cfd56_2 bioconda
bioconductor-genie3 1.16.0 r41hc0cfd56_2 bioconda
bioconductor-genomeinfodb 1.30.1 r41hdfd78af_0 bioconda
bioconductor-genomeinfodbdata 1.2.7 r41_1 pwwang
bioconductor-genomicranges 1.46.1 r41hc0cfd56_1 bioconda
bioconductor-graph 1.72.0 r41hc0cfd56_2 bioconda
bioconductor-gseabase 1.56.0 r41hdfd78af_0 bioconda
bioconductor-iranges 2.28.0 r41hc0cfd56_2 bioconda
bioconductor-keggrest 1.34.0 r41hdfd78af_0 bioconda
bioconductor-matrixgenerics 1.6.0 r41hdfd78af_0 bioconda
bioconductor-rcistarget 1.14.0 r41hdfd78af_0 bioconda
bioconductor-s4vectors 0.32.4 r41hc0cfd56_0 bioconda
bioconductor-singlecellexperiment 1.16.0 r41hdfd78af_0 bioconda
bioconductor-summarizedexperiment 1.24.0 r41hdfd78af_0 bioconda
bioconductor-xvector 0.34.0 r41hc0cfd56_2 bioconda
bioconductor-zlibbioc 1.40.0 r41hc0cfd56_2 bioconda
bokeh 2.3.3 pypi_0 pypi
boltons 23.0.0 pypi_0 pypi
brotlipy 0.7.0 py36h8f6f2f9_1001 conda-forge
bwidget 1.9.14 ha770c72_1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
c-ares 1.18.1 h7f98852_0 conda-forge
ca-certificates 2023.01.10 h06a4308_0 defaults
cached-property 1.5.2 pypi_0 pypi
cairo 1.16.0 ha61ee94_1014 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
certifi 2022.12.7 pypi_0 pypi
cffi 1.14.6 py36hd8eec40_1 conda-forge
charset-normalizer 2.0.12 pypi_0 pypi
click 8.0.4 pypi_0 pypi
cloudpickle 2.2.1 pypi_0 pypi
colorama 0.4.5 pyhd8ed1ab_0 conda-forge
conda 4.10.3 py36h5fab9bb_2 conda-forge
conda-package-handling 1.7.3 py36h8f6f2f9_0 conda-forge
contextvars 2.4 pypi_0 pypi
cryptography 35.0.0 py36hb60f036_0 conda-forge
ctxcore 0.1.1 pypi_0 pypi
curl 7.86.0 h7bff187_1 conda-forge
cytoolz 0.12.1 pypi_0 pypi
dask 2021.3.0 pypi_0 pypi
decorator 4.4.2 pypi_0 pypi
dill 0.3.4 pypi_0 pypi
distributed 2021.3.0 pypi_0 pypi
expat 2.5.0 hcb278e6_1 conda-forge
font-ttf-dejavu-sans-mono 2.37 hab24e00_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
font-ttf-inconsolata 3.000 h77eed37_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
font-ttf-source-code-pro 2.038 h77eed37_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
font-ttf-ubuntu 0.83 hab24e00_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
fontconfig 2.14.1 hc2a2eb6_0 conda-forge
fonts-conda-ecosystem 1 0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
fonts-conda-forge 1 0 conda-forge
freetype 2.12.1 hca18f0e_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
fribidi 1.0.10 h36c2ea0_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
frozendict 2.3.5 pypi_0 pypi
frozenlist 1.2.0 pypi_0 pypi
fsspec 2022.1.0 pypi_0 pypi
gcc_impl_linux-64 12.2.0 hcc96c02_19 conda-forge
geos 3.11.2 hcb278e6_0 conda-forge
gettext 0.21.1 h27087fc_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
gflags 2.2.2 he1b5a44_1004 conda-forge
gfortran_impl_linux-64 12.2.0 h55be85b_19 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
glib 2.74.1 h6239696_1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
glib-tools 2.74.1 h6239696_1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
glog 0.6.0 h6f12383_0 conda-forge
glpk 5.0 h445213a_0 conda-forge
gmp 6.2.1 h58526e2_0 conda-forge
graphite2 1.3.13 h58526e2_1001 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
gsl 2.7 he838d99_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
gxx_impl_linux-64 12.2.0 hcc96c02_19 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
h5py 3.1.0 pypi_0 pypi
harfbuzz 5.3.0 h418a68e_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
hdf5 1.12.2 nompi_h2386368_100 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
heapdict 1.0.1 pypi_0 pypi
icu 70.1 h27087fc_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
idna 3.4 pyhd8ed1ab_0 conda-forge
idna-ssl 1.1.0 pypi_0 pypi
immutables 0.19 pypi_0 pypi
importlib-metadata 4.8.3 pypi_0 pypi
importlib-resources 5.4.0 pypi_0 pypi
interlap 0.2.7 pypi_0 pypi
jinja2 3.0.3 pypi_0 pypi
joblib 1.1.1 pypi_0 pypi
jpeg 9e h0b41bf4_3 conda-forge
kernel-headers_linux-64 2.6.32 he073ed8_15 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
krb5 1.19.3 h3790be6_0 conda-forge
ld_impl_linux-64 2.39 hc81fddc_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
lerc 4.0.0 h27087fc_0 conda-forge
libabseil 20220623.0 cxx17_h05df665_6 conda-forge
libarchive 3.5.2 hb890918_3 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libarrow 10.0.1 hee49ebd_4_cpu conda-forge
libblas 3.9.0 16_linux64_openblas conda-forge
libbrotlicommon 1.0.9 h166bdaf_8 conda-forge
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libcblas 3.9.0 16_linux64_openblas conda-forge
libcrc32c 1.1.2 h9c3ff4c_0 conda-forge
libcurl 7.86.0 h7bff187_1 conda-forge
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libgcc-devel_linux-64 12.2.0 h3b97bd3_19 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
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libglib 2.74.1 h7a41b64_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libgomp 12.2.0 h65d4601_19 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libgoogle-cloud 2.5.0 h5d50b59_1 conda-forge
libgrpc 1.51.1 h05bd8bd_0 conda-forge
libiconv 1.17 h166bdaf_0 conda-forge
liblapack 3.9.0 16_linux64_openblas conda-forge
libnghttp2 1.47.0 hdcd2b5c_1 conda-forge
libnsl 2.0.0 h7f98852_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libopenblas 0.3.21 pthreads_h78a6416_3 conda-forge
libpng 1.6.39 h753d276_0 conda-forge
libprotobuf 3.21.12 h3eb15da_0 conda-forge
libsanitizer 12.2.0 h46fd767_19 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libsolv 0.7.22 h6239696_0 conda-forge
libsqlite 3.40.0 h753d276_0 conda-forge
libssh2 1.10.0 haa6b8db_3 conda-forge
libstdcxx-devel_linux-64 12.2.0 h3b97bd3_19 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libstdcxx-ng 12.2.0 h46fd767_19 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libthrift 0.16.0 h491838f_2 conda-forge
libtiff 4.4.0 h55922b4_4 conda-forge
libutf8proc 2.8.0 h166bdaf_0 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libwebp-base 1.2.4 h166bdaf_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libxcb 1.13 h7f98852_1004 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libxml2 2.10.3 h7463322_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
libzlib 1.2.13 h166bdaf_4 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
llvmlite 0.36.0 pypi_0 pypi
locket 1.0.0 pypi_0 pypi
loompy 3.0.7 pypi_0 pypi
lz4-c 1.9.3 h9c3ff4c_1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
lzo 2.10 h516909a_1000 conda-forge
make 4.3 hd18ef5c_1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
mamba 0.7.6 py36hb90a75f_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
markupsafe 2.0.1 pypi_0 pypi
msgpack 1.0.5 pypi_0 pypi
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multidict 5.2.0 pypi_0 pypi
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ncurses 6.3 h27087fc_1 conda-forge
networkx 2.5.1 pypi_0 pypi
numba 0.53.1 pypi_0 pypi
numpy 1.19.5 py36hfc0c790_2 conda-forge
numpy-groupies 0.9.20 pypi_0 pypi
openssl 1.1.1t h0b41bf4_0 conda-forge
orc 1.8.2 hfdbbad2_2 conda-forge
packaging 21.3 pypi_0 pypi
pandas 1.1.5 pypi_0 pypi
pandoc 2.19.2 h32600fe_2 conda-forge
pango 1.50.11 h382ae3d_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
partd 1.2.0 pypi_0 pypi
pcre 8.45 h9c3ff4c_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pcre2 10.37 hc3806b6_1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pillow 8.4.0 pypi_0 pypi
pip 21.3.1 pyhd8ed1ab_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pixman 0.40.0 h36c2ea0_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
psutil 5.9.4 pypi_0 pypi
pthread-stubs 0.4 h36c2ea0_1001 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pyarrow 0.16.0 pypi_0 pypi
pycosat 0.6.3 py36h8f6f2f9_1006 conda-forge
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pynndescent 0.5.8 pypi_0 pypi
pyopenssl 22.0.0 pyhd8ed1ab_1 conda-forge
pyparsing 3.0.9 pypi_0 pypi
pyscenic 0.11.2 pypi_0 pypi
pysocks 1.7.1 py36h5fab9bb_3 conda-forge
python 3.6.15 hb7a2778_0_cpython https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
python-dateutil 2.8.2 pypi_0 pypi
python_abi 3.6 2_cp36m https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
pytz 2022.7.1 pypi_0 pypi
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r-abind 1.4_5 r41hc72bb7e_1004 conda-forge
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r-askpass 1.1 r41h06615bd_3 conda-forge
r-assertthat 0.2.1 r41hc72bb7e_3 conda-forge
r-backports 1.4.1 r41h06615bd_1 conda-forge
r-base 4.1.3 h7880091_3 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
r-base64enc 0.1_3 r41h06615bd_1005 conda-forge
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r-bibtex 0.5.1 r41hc72bb7e_0 conda-forge
r-bit 4.0.5 r41h06615bd_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
r-bit64 4.0.5 r41h06615bd_1 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
r-bitops 1.0_7 r41h06615bd_1 conda-forge
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r-data.table 1.14.8 r41h133d619_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
r-dbi 1.1.3 r41hc72bb7e_1 conda-forge
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r-gtools 3.9.4 r41h06615bd_0 conda-forge
r-hdf5r 1.3.8 r41haf92f5d_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
r-here 1.0.1 r41hc72bb7e_1 conda-forge
r-hexbin 1.28.3 r41hac0b197_0 conda-forge
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r-hms 1.1.3 r41hc72bb7e_0 conda-forge
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r-httpuv 1.6.9 r41h38f115c_0 conda-forge
r-httr 1.4.5 r41hc72bb7e_0 conda-forge
r-ica 1.0_3 r41hc72bb7e_1 conda-forge
r-igraph 1.4.1 r41h65ed38e_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
r-irlba 2.3.5.1 r41h5f7b363_0 conda-forge
r-isoband 0.2.7 r41h38f115c_1 conda-forge
r-iterators 1.0.14 r41hc72bb7e_1 conda-forge
r-jquerylib 0.1.4 r41hc72bb7e_1 conda-forge
r-jsonlite 1.8.4 r41h133d619_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
r-kernlab 0.9_32 r41h358215d_0 conda-forge
r-kernsmooth 2.23_20 r41hd009a43_1 conda-forge
r-knitr 1.42 r41hc72bb7e_1 conda-forge
r-labeling 0.4.2 r41hc72bb7e_2 conda-forge
r-later 1.3.0 r41h7525677_1 conda-forge
r-lattice 0.20_45 r41h06615bd_1 conda-forge
r-lazyeval 0.2.2 r41h06615bd_3 conda-forge
r-leiden 0.4.3 r41hc72bb7e_1 conda-forge
r-lifecycle 1.0.3 r41hc72bb7e_1 conda-forge
r-listenv 0.9.0 r41hc72bb7e_0 conda-forge
r-lmtest 0.9_40 r41h8da6f51_1 conda-forge
r-lsei 1.3_0 r41hc3ea6d6_2 conda-forge
r-magrittr 2.0.3 r41h06615bd_1 conda-forge
r-mass 7.3_58.3 r41h133d619_0 conda-forge
r-matrix 1.5_3 r41h5f7b363_0 conda-forge
r-matrixstats 0.63.0 r41h06615bd_0 conda-forge
r-memoise 2.0.1 r41hc72bb7e_1 conda-forge
r-mgcv 1.8_42 r41he1ae0d6_0 conda-forge
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r-miniui 0.1.1.1 r41hc72bb7e_1003 conda-forge
r-mixtools 2.0.0 r41h133d619_0 conda-forge
r-munsell 0.5.0 r41hc72bb7e_1005 conda-forge
r-nlme 3.1_162 r41hac0b197_0 conda-forge
r-nmf 0.21.0 r41h7525677_1005 conda-forge
r-npsurv 0.5_0 r41hc72bb7e_1 conda-forge
r-openssl 2.0.5 r41hb1dc35e_0 conda-forge
r-parallelly 1.35.0 r41hc72bb7e_0 conda-forge
r-patchwork 1.1.2 r41hc72bb7e_1 conda-forge
r-pbapply 1.7_0 r41hc72bb7e_0 conda-forge
r-pillar 1.9.0 r41hc72bb7e_0 conda-forge
r-pkgconfig 2.0.3 r41hc72bb7e_2 conda-forge
r-pkgmaker 0.32.8 r41hc72bb7e_0 conda-forge
r-plogr 0.2.0 r41hc72bb7e_1004 conda-forge
r-plotly 4.10.1 r41hc72bb7e_0 conda-forge
r-plyr 1.8.8 r41h7525677_0 conda-forge
r-png 0.1_8 r41h10cf519_0 conda-forge
r-polyclip 1.10_4 r41h7525677_0 conda-forge
r-progressr 0.13.0 r41hc72bb7e_0 conda-forge
r-promises 1.2.0.1 r41h7525677_1 conda-forge
r-purrr 1.0.1 r41h133d619_0 conda-forge
r-r.methodss3 1.8.2 r41hc72bb7e_1 conda-forge
r-r.oo 1.25.0 r41hc72bb7e_1 conda-forge
r-r.utils 2.12.2 r41hc72bb7e_0 conda-forge
r-r6 2.5.1 r41hc72bb7e_1 conda-forge
r-rann 2.6.1 r41h7525677_3 conda-forge
r-rappdirs 0.3.3 r41h06615bd_1 conda-forge
r-rcolorbrewer 1.1_3 r41h785f33e_1 conda-forge
r-rcpp 1.0.10 r41h38f115c_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
r-rcppannoy 0.0.20 r41h7525677_0 conda-forge
r-rcpparmadillo 0.11.4.4.0 r41h358215d_0 conda-forge
r-rcppeigen 0.3.3.9.3 r41h9f5de39_0 conda-forge
r-rcppparallel 5.1.6 r41h38f115c_0 conda-forge
r-rcppprogress 0.4.2 r41hc72bb7e_2 conda-forge
r-rcpptoml 0.1.7 r41h7525677_2 conda-forge
r-rcurl 1.98_1.12 r41h133d619_0 conda-forge
r-registry 0.5_1 r41hc72bb7e_3 conda-forge
r-reshape2 1.4.4 r41h7525677_2 conda-forge
r-reticulate 1.28 r41h38f115c_0 conda-forge
r-rgeos 0.6_2 r41h0d5128d_1 conda-forge
r-rjson 0.2.21 r41h7525677_2 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
r-rlang 1.1.0 r41h38f115c_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
r-rmarkdown 2.21 r41hc72bb7e_0 conda-forge
r-rngtools 1.5.2 r41hc72bb7e_1 conda-forge
r-rocr 1.0_11 r41hc72bb7e_2 conda-forge
r-rprojroot 2.0.3 r41hc72bb7e_1 conda-forge
r-rspectra 0.16_1 r41h9f5de39_1 conda-forge
r-rsqlite 2.3.0 r41h38f115c_0 conda-forge
r-rtsne 0.16 r41h37cf8d7_1 conda-forge
r-sass 0.4.5 r41h38f115c_0 conda-forge
r-scales 1.2.1 r41hc72bb7e_1 conda-forge
r-scattermore 0.8 r41h06615bd_1 conda-forge
r-scenic 1.1.2_01 r41_0 maximinio
r-sctransform 0.3.5 r41h9f5de39_1 conda-forge
r-segmented 1.6_3 r41hc72bb7e_0 conda-forge
r-seurat 4.3.0 r41h38f115c_0 conda-forge
r-seuratobject 4.1.3 r41h38f115c_0 conda-forge
r-shiny 1.7.4 r41h785f33e_0 conda-forge
r-sitmo 2.0.2 r41h7525677_1 conda-forge
r-sourcetools 0.1.7_1 r41h38f115c_0 conda-forge
r-sp 1.6_0 r41h133d619_0 conda-forge
r-spatstat.data 3.0_1 r41hc72bb7e_0 conda-forge
r-spatstat.explore 3.1_0 r41h133d619_0 conda-forge
r-spatstat.geom 3.1_0 r41h133d619_0 conda-forge
r-spatstat.random 3.1_4 r41h38f115c_0 conda-forge
r-spatstat.sparse 3.0_1 r41h133d619_0 conda-forge
r-spatstat.utils 3.0_2 r41h133d619_0 conda-forge
r-stringi 1.7.12 r41h1ae9187_0 conda-forge
r-stringr 1.5.0 r41h785f33e_0 conda-forge
r-survival 3.5_5 r41h133d619_0 conda-forge
r-sys 3.4.1 r41h06615bd_0 conda-forge
r-tensor 1.5 r41hc72bb7e_1004 conda-forge
r-tibble 3.2.1 r41h133d619_1 conda-forge
r-tidyr 1.3.0 r41h38f115c_0 conda-forge
r-tidyselect 1.2.0 r41hc72bb7e_0 conda-forge
r-tinytex 0.44 r41hc72bb7e_0 conda-forge
r-utf8 1.2.3 r41h133d619_0 conda-forge
r-uwot 0.1.14 r41h7525677_1 conda-forge
r-vctrs 0.6.1 r41h38f115c_0 conda-forge
r-viridislite 0.4.1 r41hc72bb7e_1 conda-forge
r-withr 2.5.0 r41hc72bb7e_1 conda-forge
r-xfun 0.38 r41h38f115c_0 conda-forge
r-xml 3.99_0.14 r41hb43fdd4_0 conda-forge
r-xml2 1.3.3 r41h044e5c7_2 conda-forge
r-xtable 1.8_4 r41hc72bb7e_4 conda-forge
r-yaml 2.3.7 r41h133d619_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
r-zoo 1.8_11 r41h06615bd_1 conda-forge
re2 2022.06.01 h27087fc_1 conda-forge
readline 8.1.2 h0f457ee_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
reproc 14.2.3 h7f98852_0 conda-forge
reproc-cpp 14.2.3 h9c3ff4c_0 conda-forge
requests 2.27.1 pypi_0 pypi
ruamel_yaml 0.15.80 py36h8f6f2f9_1004 conda-forge
s2n 1.3.30 hae46d1a_0 conda-forge
scikit-learn 0.24.2 pypi_0 pypi
scipy 1.5.4 pypi_0 pypi
sed 4.8 he412f7d_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
setuptools 58.0.4 py36h5fab9bb_2 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
snappy 1.1.10 h9fff704_0 conda-forge
sortedcontainers 2.4.0 pypi_0 pypi
sqlite 3.40.0 h4ff8645_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
sysroot_linux-64 2.12 he073ed8_15 conda-forge
tblib 1.7.0 pypi_0 pypi
threadpoolctl 3.1.0 pypi_0 pypi
tk 8.6.12 h27826a3_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
tktable 2.10 hb7b940f_3 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
toolz 0.12.0 pypi_0 pypi
tornado 6.1 pypi_0 pypi
tqdm 4.7.2 py36_0 bioconda
typing-extensions 4.1.1 pypi_0 pypi
umap-learn 0.5.3 pypi_0 pypi
urllib3 1.26.15 pypi_0 pypi
wheel 0.37.1 pyhd8ed1ab_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
xorg-kbproto 1.0.7 h7f98852_1002 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
xorg-libice 1.0.10 h7f98852_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
xorg-libsm 1.2.3 hd9c2040_1000 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
xorg-libx11 1.8.4 h0b41bf4_0 conda-forge
xorg-libxau 1.0.9 h7f98852_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
xorg-libxext 1.3.4 h0b41bf4_2 conda-forge
xorg-libxrender 0.9.10 h7f98852_1003 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
xorg-libxt 1.2.1 h7f98852_2 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
xorg-renderproto 0.11.1 h7f98852_1002 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
xorg-xextproto 7.3.0 h0b41bf4_1003 conda-forge
xorg-xproto 7.0.31 h7f98852_1007 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
xz 5.2.6 h166bdaf_0 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
yaml 0.2.5 h7f98852_2 conda-forge
yarl 1.7.2 pypi_0 pypi
zict 2.1.0 pypi_0 pypi
zipp 3.6.0 pypi_0 pypi
zlib 1.2.13 h166bdaf_4 conda-forge
zstd 1.5.2 h6239696_4 https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
the same issue
This is probably the wrong version of python or package, this issue disappeared after I re-downloaded python=3.10 and pyscenic (my previous python version was 3.6)
Latest provided Feather files are in v2 format (are in Arrow IPC format). and require pySCENIC >= 0.12.x
In the pySCENIC v0.12.0 release notes, you can see:
Only databases in Feather v2 format are supported now (ctxcore >= 0.2), which allow uses recent versions of pyarrow (>=8.0.0) instead of very old ones (<0.17). Databases in the new format can be downloaded from https://resources.aertslab.org/cistarget/databases/ and end with *.genes_vs_motifs.rankings.feather or *.genes_vs_tracks.rankings.feather.
If you wanna use pySCENIC version: 0.11.2, you can use old version data in https://resources.aertslab.org/cistarget/databases/old
