Description
Running phy template-gui ./params.py --debug gives this output:
11:51:49.131 [D] init:68 Start capturing exceptions.
11:51:49.202 [D] model:619 Loading spike clusters.
11:51:49.250 [D] model:692 Loading templates.
11:51:49.265 [D] model:724 Templates are dense.
11:51:49.267 [W] model:667 Skipping spike waveforms that do not exist, they will be extracted on the fly from the raw data as needed.
11:51:49.267 [D] model:730 Loading the whitening matrix.
11:51:49.268 [D] model:737 Loading the inverse of the whitening matrix.
11:51:49.271 [W] model:455 There are 1635641/1806190 spikes after the end of the recording.
11:51:49.271 [D] model:766 Loading features.
11:51:49.271 [D] model:781 Features are sparse.
11:51:49.272 [D] model:803 Loading template features.
11:51:49.274 [D] model:530 Load spike_detection_templates.npy.
11:51:49.282 [D] model:530 Load spike_positions.npy.
11:51:49.283 [D] model:504 Load cluster_Amplitude.tsv.
11:51:49.284 [D] model:504 Load cluster_ContamPct.tsv.
11:51:49.285 [D] model:504 Load cluster_KSLabel.tsv.
11:51:49.286 [D] model:504 Load cluster_group.tsv.
11:51:49.505 [D] context:100 Initialize joblib cache dir at /home/ucsc/ks_data/kilosort4/.phy.
11:51:49.505 [D] context:101 Reducing the size of the cache if needed.
11:51:49.506 [D] base:102 Add filter high_pass.
11:51:49.506 [D] config:31 Load config file /home/ucsc/.phy/phy_config.py.
11:51:49.506 [D] plugin:146 Loading 0 plugins.
11:51:49.507 [D] context:209 The file /home/ucsc/ks_data/kilosort4/.phy/new_cluster_id.pkl doesn't exist.
11:51:49.551 [D] context:185 Save data to /home/ucsc/ks_data/kilosort4/.phy/spikes_per_cluster.pkl.
11:51:49.618 [D] gui:463 Creating GUI.
11:51:49.623 [D] state:46 Load /home/ucsc/.phy/TemplateGUI/state.json for GUIState.
11:51:50.173 [D] gui:718 Add view ClusterView to GUI.
11:51:50.178 [D] gui:718 Add view SimilarityView to GUI.
11:51:50.208 [D] gui:718 Add view WaveformView to GUI.
11:51:50.210 [D] base:337 Set state for WaveformView.
11:51:50.220 [D] gui:718 Add view CorrelogramView to GUI.
11:51:50.221 [D] base:337 Set state for CorrelogramView.
11:51:50.240 [D] gui:718 Add view ISIView to GUI.
11:51:50.242 [D] base:337 Set state for ISIView.
11:51:50.251 [D] gui:718 Add view FeatureView to GUI.
11:51:50.253 [D] base:337 Set state for FeatureView.
Segmentation fault (core dumped)
My conda environment is using this version of python:
Python 3.11.10
Conda list output:
Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
arrow-cpp 16.1.0 hc1eb8f0_0
asttokens 2.0.5 pyhd3eb1b0_0
aws-c-auth 0.6.19 h5eee18b_0
aws-c-cal 0.5.20 hdbd6064_0
aws-c-common 0.8.5 h5eee18b_0
aws-c-compression 0.2.16 h5eee18b_0
aws-c-event-stream 0.2.15 h6a678d5_0
aws-c-http 0.6.25 h5eee18b_0
aws-c-io 0.13.10 h5eee18b_0
aws-c-mqtt 0.7.13 h5eee18b_0
aws-c-s3 0.1.51 hdbd6064_0
aws-c-sdkutils 0.1.6 h5eee18b_0
aws-checksums 0.1.13 h5eee18b_0
aws-crt-cpp 0.18.16 h6a678d5_0
aws-sdk-cpp 1.10.55 h721c034_0
blas 1.0 mkl
bokeh 3.6.0 py311h06a4308_0
boost-cpp 1.82.0 hdb19cb5_2
bottleneck 1.3.7 py311hf4808d0_0
brotli 1.0.9 h5eee18b_8
brotli-bin 1.0.9 h5eee18b_8
brotli-python 1.0.9 py311h6a678d5_8
bzip2 1.0.8 h5eee18b_6
c-ares 1.19.1 h5eee18b_0
ca-certificates 2024.9.24 h06a4308_0
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
certifi 2024.8.30 pyhd8ed1ab_0 conda-forge
charset-normalizer 3.3.2 pyhd3eb1b0_0
click 8.1.7 py311h06a4308_0
cloudpickle 3.0.0 py311h06a4308_0
colorama 0.4.6 pyhd8ed1ab_0 conda-forge
colorcet 3.1.0 pypi_0 pypi
comm 0.2.1 py311h06a4308_0
contourpy 1.2.0 py311hdb19cb5_0
cycler 0.11.0 pyhd3eb1b0_0
cyrus-sasl 2.1.28 h52b45da_1
cython 3.0.11 py311h55d416d_3 conda-forge
cytoolz 0.12.2 py311h5eee18b_0
dask 2024.10.0 pyhd8ed1ab_0 conda-forge
dask-core 2024.10.0 pyhd8ed1ab_0 conda-forge
dask-expr 1.1.16 pyhd8ed1ab_0 conda-forge
dbus 1.13.18 hb2f20db_0
debugpy 1.6.7 py311h6a678d5_0
decorator 5.1.1 pyhd3eb1b0_0
distributed 2024.10.0 pyhd8ed1ab_0 conda-forge
exceptiongroup 1.2.2 pyhd8ed1ab_0 conda-forge
executing 0.8.3 pyhd3eb1b0_0
expat 2.6.3 h6a678d5_0
fontconfig 2.14.1 h4c34cd2_2
fonttools 4.51.0 py311h5eee18b_0
freetype 2.12.1 h4a9f257_0
fsspec 2024.6.1 py311h06a4308_0
gflags 2.2.2 h6a678d5_1
ghp-import 2.1.0 pypi_0 pypi
git 2.45.1 pl5321hef9f9f3_0 conda-forge
glib 2.80.2 hf974151_0 conda-forge
glib-tools 2.80.2 hb6ce0ca_0 conda-forge
glog 0.5.0 h6a678d5_1
gst-plugins-base 1.14.1 h6a678d5_1
gstreamer 1.14.1 h5eee18b_1
h5py 3.12.1 nompi_py311hb639ac4_101 conda-forge
hdf5 1.14.3 nompi_hdf9ad27_105 conda-forge
heapdict 1.0.1 pyhd3eb1b0_0
icu 73.1 h6a678d5_0
idna 3.7 py311h06a4308_0
importlib-metadata 7.0.1 py311h06a4308_0
importlib_metadata 7.0.1 hd8ed1ab_0 conda-forge
iniconfig 1.1.1 pyhd3eb1b0_0
intel-openmp 2023.1.0 hdb19cb5_46306
ipykernel 6.29.5 py311h06a4308_0
ipython 8.27.0 py311h06a4308_0
jedi 0.19.1 py311h06a4308_0
jinja2 3.1.4 py311h06a4308_0
joblib 1.4.2 pyhd8ed1ab_0 conda-forge
jpeg 9e h5eee18b_3
jupyter_client 8.6.0 py311h06a4308_0
jupyter_core 5.7.2 py311h06a4308_0
kiwisolver 1.4.4 py311h6a678d5_0
krb5 1.20.1 h143b758_1
lcms2 2.12 h3be6417_0
ld_impl_linux-64 2.40 h12ee557_0
lerc 3.0 h295c915_0
libabseil 20240116.2 cxx17_h6a678d5_0
libaec 1.1.3 h59595ed_0 conda-forge
libblas 3.9.0 1_h86c2bf4_netlib conda-forge
libboost 1.82.0 h109eef0_2
libbrotlicommon 1.0.9 h5eee18b_8
libbrotlidec 1.0.9 h5eee18b_8
libbrotlienc 1.0.9 h5eee18b_8
libcblas 3.9.0 7_ha36c22a_netlib conda-forge
libclang 14.0.6 default_hc6dbbc7_1
libclang13 14.0.6 default_he11475f_1
libcups 2.4.2 h2d74bed_1
libcurl 8.9.1 h251f7ec_0
libdeflate 1.17 h5eee18b_1
libedit 3.1.20230828 h5eee18b_0
libev 4.33 h7f8727e_1
libevent 2.1.12 hdbd6064_1
libexpat 2.6.3 h5888daf_0 conda-forge
libffi 3.4.4 h6a678d5_1
libgcc 14.2.0 h77fa898_1 conda-forge
libgcc-ng 14.2.0 h69a702a_1 conda-forge
libgfortran 14.2.0 h69a702a_1 conda-forge
libgfortran-ng 14.2.0 h69a702a_1 conda-forge
libgfortran5 14.2.0 hd5240d6_1 conda-forge
libglib 2.80.2 hf974151_0 conda-forge
libgomp 14.2.0 h77fa898_1 conda-forge
libgrpc 1.62.2 h2d74bed_0
libiconv 1.17 hd590300_2 conda-forge
liblapack 3.9.0 7_ha36c22a_netlib conda-forge
libllvm14 14.0.6 hecde1de_4
libnghttp2 1.57.0 h2d74bed_0
libpng 1.6.39 h5eee18b_0
libpq 12.17 hdbd6064_0
libprotobuf 4.25.3 he621ea3_0
libsodium 1.0.18 h7b6447c_0
libssh2 1.11.0 h251f7ec_0
libstdcxx 14.2.0 hc0a3c3a_1 conda-forge
libstdcxx-ng 14.2.0 h4852527_1 conda-forge
libthrift 0.15.0 h1795dd8_2
libtiff 4.5.1 h6a678d5_0
libuuid 1.41.5 h5eee18b_0
libwebp-base 1.3.2 h5eee18b_1
libxcb 1.15 h7f8727e_0
libxcrypt 4.4.36 hd590300_1 conda-forge
libxkbcommon 1.0.1 h5eee18b_1
libxml2 2.10.4 hfdd30dd_2
libzlib 1.2.13 h4ab18f5_6 conda-forge
locket 1.0.0 py311h06a4308_0
lz4 4.3.2 py311h5eee18b_0
lz4-c 1.9.4 h6a678d5_1
markdown 3.7 pypi_0 pypi
markupsafe 2.1.3 py311h5eee18b_0
matplotlib 3.9.2 py311h06a4308_0
matplotlib-base 3.9.2 py311h6fb44e5_0
matplotlib-inline 0.1.6 py311h06a4308_0
mergedeep 1.3.4 pypi_0 pypi
mkdocs 1.6.1 pypi_0 pypi
mkdocs-get-deps 0.2.0 pypi_0 pypi
mkl 2023.1.0 h213fc3f_46344
mkl-service 2.4.0 py311h5eee18b_1
mkl_fft 1.3.10 py311h5eee18b_0
mkl_random 1.2.7 py311ha02d727_0
msgpack-python 1.0.3 py311hdb19cb5_0
mtscomp 1.0.2 pypi_0 pypi
mysql 5.7.24 h721c034_2
ncurses 6.4 h6a678d5_0
nest-asyncio 1.6.0 py311h06a4308_0
nspr 4.35 h6a678d5_0
nss 3.89.1 h6a678d5_0
numexpr 2.8.7 py311h65dcdc2_0
numpy 1.26.4 py311h08b1b3b_0
numpy-base 1.26.4 py311hf175353_0
openjpeg 2.5.2 he7f1fd0_0
openssl 3.3.2 hb9d3cd8_0 conda-forge
orc 2.0.1 h2d29ad5_0
packaging 24.1 py311h06a4308_0
pandas 2.2.2 py311ha02d727_0
parso 0.8.3 pyhd3eb1b0_0
partd 1.4.1 py311h06a4308_0
pathspec 0.12.1 pypi_0 pypi
pcre2 10.43 hcad00b1_0 conda-forge
perl 5.32.1 7_hd590300_perl5 conda-forge
pexpect 4.8.0 pyhd3eb1b0_3
phy 2.0b6 pypi_0 pypi
phylib 2.6.0 pypi_0 pypi
pillow 10.4.0 py311h5eee18b_0
pip 24.2 pyh8b19718_1 conda-forge
platformdirs 3.10.0 py311h06a4308_0
pluggy 1.5.0 pyhd8ed1ab_0 conda-forge
ply 3.11 py311h06a4308_0
prompt-toolkit 3.0.43 py311h06a4308_0
prompt_toolkit 3.0.43 hd3eb1b0_0
psutil 5.9.0 py311h5eee18b_0
ptyprocess 0.7.0 pyhd3eb1b0_2
pure_eval 0.2.2 pyhd3eb1b0_0
pyarrow 16.1.0 py311ha02d727_0
pybind11-abi 4 hd3eb1b0_1
pygments 2.15.1 py311h06a4308_1
pyopengl 3.1.6 pyhd8ed1ab_1 conda-forge
pyparsing 3.1.2 py311h06a4308_0
pyqt 5.15.10 py311h6a678d5_0
pyqt5-sip 12.13.0 py311h5eee18b_0
pyqtwebengine 5.15.10 py311h6a678d5_0
pysocks 1.7.1 py311h06a4308_0
pytest 8.3.3 pyhd8ed1ab_0 conda-forge
python 3.11.10 he870216_0
python-dateutil 2.9.0post0 py311h06a4308_2
python-lmdb 1.4.1 py311h6a678d5_0
python-tzdata 2023.3 pyhd3eb1b0_0
python_abi 3.11 2_cp311 conda-forge
pytz 2024.1 py311h06a4308_0
pyyaml 6.0.2 py311h5eee18b_0
pyyaml-env-tag 0.1 pypi_0 pypi
pyzmq 25.1.2 py311h6a678d5_0
qt-main 5.15.2 h53bd1ea_10
qt-webengine 5.15.9 h9ab4d14_7
qtconsole 5.6.0 pyhd8ed1ab_0 conda-forge
qtconsole-base 5.6.0 pyha770c72_0 conda-forge
qtpy 2.4.1 py311h06a4308_0
re2 2022.04.01 h295c915_0
readline 8.2 h5eee18b_0
requests 2.32.3 pyhd8ed1ab_0 conda-forge
responses 0.25.3 pyhd8ed1ab_0 conda-forge
s2n 1.3.27 hdbd6064_0
scikit-learn 1.5.2 py311h57cc02b_1 conda-forge
scipy 1.14.1 py311he1f765f_0 conda-forge
setuptools 75.1.0 py311h06a4308_0
sip 6.7.12 py311h6a678d5_0
six 1.16.0 pyhd3eb1b0_1
snappy 1.2.1 h6a678d5_0
sortedcontainers 2.4.0 pyhd3eb1b0_0
sqlite 3.45.3 h5eee18b_0
stack_data 0.2.0 pyhd3eb1b0_0
tbb 2021.8.0 hdb19cb5_0
tblib 1.7.0 pyhd3eb1b0_0
threadpoolctl 3.5.0 py311h92b7b1e_0
tk 8.6.14 h39e8969_0
tomli 2.0.2 pyhd8ed1ab_0 conda-forge
toolz 0.12.0 py311h06a4308_0
tornado 6.4.1 py311h5eee18b_0
tqdm 4.66.5 pypi_0 pypi
traitlets 5.14.3 pyhd8ed1ab_0 conda-forge
types-pyyaml 6.0.12.20240917 pyhd8ed1ab_0 conda-forge
typing_extensions 4.11.0 py311h06a4308_0
tzdata 2024b h04d1e81_0
unicodedata2 15.1.0 py311h5eee18b_0
urllib3 2.2.3 py311h06a4308_0
utf8proc 2.6.1 h5eee18b_1
watchdog 5.0.3 pypi_0 pypi
wcwidth 0.2.5 pyhd3eb1b0_0
wheel 0.44.0 py311h06a4308_0
xyzservices 2022.9.0 py311h06a4308_1
xz 5.4.6 h5eee18b_1
yaml 0.2.5 h7b6447c_0
zeromq 4.3.5 h6a678d5_0
zict 3.0.0 py311h06a4308_0
zipp 3.20.2 py311h06a4308_0
zlib 1.2.13 h4ab18f5_6 conda-forge
zstd 1.5.6 hc292b87_0
I was wondering if I could get some help remedying this?
I am using Ubuntu 20.04