I recently upgraded the OS in my pc to Fedora 35. In Fedora 34 phy was working fine. But now I get a 'Failed to establish dbus connection' error when running phy. Here is the output of phy template-gui params.py --debug
11:27:05.777 [D] __init__:68 Start capturing exceptions. 11:27:05.787 [D] model:607 Loading spike clusters. 11:27:05.793 [D] model:680 Loading templates. 11:27:05.794 [D] model:705 Templates are sparse. 11:27:05.794 [W] model:656 Skipping spike waveforms that do not exist, they will be extracted on the fly from the raw data as needed. 11:27:05.794 [D] model:715 Loading the whitening matrix. 11:27:05.794 [D] model:722 Loading the inverse of the whitening matrix. 11:27:05.795 [D] model:751 Loading features. 11:27:05.795 [D] model:788 Loading template features. 11:27:05.796 [D] model:492 Loadcluster_purity.tsv. Failed to establish dbus connection11:27:05.979 [D] context:100 Initialize joblib cache dir at/home/molel/spyking-circus/E16_22_05_21/E16_22_05_21/E16_22_05_21-1-final.GUI/.phy. 11:27:05.980 [D] context:101 Reducing the size of the cache if needed. 11:27:06.019 [D] base:102 Add filterhigh_pass. 11:27:06.019 [D] config:31 Load config file/home/molel/.phy/phy_config.py. 11:27:06.019 [D] plugin:145 Loading 0 plugins. 11:27:06.020 [D] context:126 Load memcache forphy.apps.base._get_mean_waveforms. 11:27:06.020 [D] context:126 Load memcache forphy.apps.base._get_mean_waveforms. 11:27:06.021 [D] context:126 Load memcache forphy.apps.base._get_template_waveforms. 11:27:06.021 [D] context:126 Load memcache forphy.apps.base.get_mean_spike_template_amplitudes. 11:27:06.021 [D] context:126 Load memcache forphy.apps.base.get_template_counts. 11:27:06.021 [D] context:126 Load memcache forphy.apps.base.get_template_for_cluster. 11:27:06.022 [D] context:126 Load memcache forphy.apps.template.gui.get_template_amplitude. 11:27:06.022 [D] context:126 Load memcache forphy.apps.base.get_cluster_amplitude. 11:27:06.022 [D] context:126 Load memcache forphy.apps.base.get_mean_firing_rate. 11:27:06.022 [D] context:126 Load memcache forphy.apps.base.get_best_channel. 11:27:06.022 [D] context:126 Load memcache forphy.apps.template.gui.get_best_channels. 11:27:06.023 [D] context:126 Load memcache forphy.apps.base.get_channel_shank. 11:27:06.023 [D] context:126 Load memcache forphy.apps.base.get_probe_depth. 11:27:06.023 [D] context:126 Load memcache forphy.apps.base.peak_channel_similarity. 11:27:06.023 [D] context:209 The file/home/molel/spyking-circus/E16_22_05_21/E16_22_05_21/E16_22_05_21-1-final.GUI/.phy/new_cluster_id.pkldoesn't exist. 11:27:06.029 [D] context:185 Save data to/home/molel/spyking-circus/E16_22_05_21/E16_22_05_21/E16_22_05_21-1-final.GUI/.phy/spikes_per_cluster.pkl. 11:27:06.037 [D] gui:463 Creating GUI. 11:27:06.038 [D] state:46 Load /home/molel/.phy/TemplateGUI/state.json for GUIState. 11:27:06.038 [D] state:46 Load /home/molel/spyking-circus/E16_22_05_21/E16_22_05_21/E16_22_05_21-1-final.GUI/.phy/state.json for GUIState. 11:27:06.104 [D] gui:718 Add view ClusterView to GUI. 11:27:06.115 [D] gui:718 Add view SimilarityView to GUI. 11:27:06.142 [D] gui:718 Add view WaveformView to GUI. 11:27:06.144 [D] base:334 Set state for WaveformView. 11:27:06.153 [D] gui:718 Add view CorrelogramView to GUI. 11:27:06.154 [D] base:334 Set state for CorrelogramView. 11:27:06.162 [D] gui:718 Add view CorrelogramView to GUI. 11:27:06.163 [D] base:334 Set state for CorrelogramView (1). 11:27:06.170 [D] gui:718 Add view CorrelogramView to GUI. 11:27:06.172 [D] base:334 Set state for CorrelogramView (2). 11:27:06.179 [D] gui:718 Add view CorrelogramView to GUI. 11:27:06.180 [D] base:334 Set state for CorrelogramView (3). 11:27:06.187 [D] gui:718 Add view CorrelogramView to GUI. 11:27:06.188 [D] base:334 Set state for CorrelogramView (4). 11:27:06.205 [D] gui:718 Add view ISIView to GUI. 11:27:06.206 [D] base:334 Set state for ISIView. 11:27:06.221 [D] gui:718 Add view ISIView to GUI. 11:27:06.222 [D] base:334 Set state for ISIView (1). 11:27:06.238 [D] gui:718 Add view AmplitudeView to GUI. 11:27:06.239 [D] base:334 Set state for AmplitudeView. 11:27:06.255 [D] gui:718 Add view AmplitudeView to GUI. 11:27:06.256 [D] base:334 Set state for AmplitudeView (1). 11:27:06.273 [D] gui:718 Add view AmplitudeView to GUI. 11:27:06.275 [D] base:334 Set state for AmplitudeView (2). 11:27:06.293 [D] gui:718 Add view AmplitudeView to GUI. 11:27:06.294 [D] base:334 Set state for AmplitudeView (3). 11:27:06.345 [D] gui:718 Add view ProbeView to GUI. 11:27:06.346 [D] base:334 Set state for ProbeView. 11:27:06.358 [D] gui:718 Add view ProbeView to GUI. 11:27:06.359 [D] base:334 Set state for ProbeView (1). 11:27:06.670 [D] gui:519 Load the geometry state.
I recently upgraded the OS in my pc to Fedora 35. In Fedora 34 phy was working fine. But now I get a 'Failed to establish dbus connection' error when running phy. Here is the output of phy template-gui params.py --debug
11:27:05.777 [D] __init__:68 Start capturing exceptions. 11:27:05.787 [D] model:607 Loading spike clusters. 11:27:05.793 [D] model:680 Loading templates. 11:27:05.794 [D] model:705 Templates are sparse. 11:27:05.794 [W] model:656 Skipping spike waveforms that do not exist, they will be extracted on the fly from the raw data as needed. 11:27:05.794 [D] model:715 Loading the whitening matrix. 11:27:05.794 [D] model:722 Loading the inverse of the whitening matrix. 11:27:05.795 [D] model:751 Loading features. 11:27:05.795 [D] model:788 Loading template features. 11:27:05.796 [D] model:492 Loadcluster_purity.tsv. Failed to establish dbus connection11:27:05.979 [D] context:100 Initialize joblib cache dir at/home/molel/spyking-circus/E16_22_05_21/E16_22_05_21/E16_22_05_21-1-final.GUI/.phy. 11:27:05.980 [D] context:101 Reducing the size of the cache if needed. 11:27:06.019 [D] base:102 Add filterhigh_pass. 11:27:06.019 [D] config:31 Load config file/home/molel/.phy/phy_config.py. 11:27:06.019 [D] plugin:145 Loading 0 plugins. 11:27:06.020 [D] context:126 Load memcache forphy.apps.base._get_mean_waveforms. 11:27:06.020 [D] context:126 Load memcache forphy.apps.base._get_mean_waveforms. 11:27:06.021 [D] context:126 Load memcache forphy.apps.base._get_template_waveforms. 11:27:06.021 [D] context:126 Load memcache forphy.apps.base.get_mean_spike_template_amplitudes. 11:27:06.021 [D] context:126 Load memcache forphy.apps.base.get_template_counts. 11:27:06.021 [D] context:126 Load memcache forphy.apps.base.get_template_for_cluster. 11:27:06.022 [D] context:126 Load memcache forphy.apps.template.gui.get_template_amplitude. 11:27:06.022 [D] context:126 Load memcache forphy.apps.base.get_cluster_amplitude. 11:27:06.022 [D] context:126 Load memcache forphy.apps.base.get_mean_firing_rate. 11:27:06.022 [D] context:126 Load memcache forphy.apps.base.get_best_channel. 11:27:06.022 [D] context:126 Load memcache forphy.apps.template.gui.get_best_channels. 11:27:06.023 [D] context:126 Load memcache forphy.apps.base.get_channel_shank. 11:27:06.023 [D] context:126 Load memcache forphy.apps.base.get_probe_depth. 11:27:06.023 [D] context:126 Load memcache forphy.apps.base.peak_channel_similarity. 11:27:06.023 [D] context:209 The file/home/molel/spyking-circus/E16_22_05_21/E16_22_05_21/E16_22_05_21-1-final.GUI/.phy/new_cluster_id.pkldoesn't exist. 11:27:06.029 [D] context:185 Save data to/home/molel/spyking-circus/E16_22_05_21/E16_22_05_21/E16_22_05_21-1-final.GUI/.phy/spikes_per_cluster.pkl. 11:27:06.037 [D] gui:463 Creating GUI. 11:27:06.038 [D] state:46 Load /home/molel/.phy/TemplateGUI/state.json for GUIState. 11:27:06.038 [D] state:46 Load /home/molel/spyking-circus/E16_22_05_21/E16_22_05_21/E16_22_05_21-1-final.GUI/.phy/state.json for GUIState. 11:27:06.104 [D] gui:718 Add view ClusterView to GUI. 11:27:06.115 [D] gui:718 Add view SimilarityView to GUI. 11:27:06.142 [D] gui:718 Add view WaveformView to GUI. 11:27:06.144 [D] base:334 Set state for WaveformView. 11:27:06.153 [D] gui:718 Add view CorrelogramView to GUI. 11:27:06.154 [D] base:334 Set state for CorrelogramView. 11:27:06.162 [D] gui:718 Add view CorrelogramView to GUI. 11:27:06.163 [D] base:334 Set state for CorrelogramView (1). 11:27:06.170 [D] gui:718 Add view CorrelogramView to GUI. 11:27:06.172 [D] base:334 Set state for CorrelogramView (2). 11:27:06.179 [D] gui:718 Add view CorrelogramView to GUI. 11:27:06.180 [D] base:334 Set state for CorrelogramView (3). 11:27:06.187 [D] gui:718 Add view CorrelogramView to GUI. 11:27:06.188 [D] base:334 Set state for CorrelogramView (4). 11:27:06.205 [D] gui:718 Add view ISIView to GUI. 11:27:06.206 [D] base:334 Set state for ISIView. 11:27:06.221 [D] gui:718 Add view ISIView to GUI. 11:27:06.222 [D] base:334 Set state for ISIView (1). 11:27:06.238 [D] gui:718 Add view AmplitudeView to GUI. 11:27:06.239 [D] base:334 Set state for AmplitudeView. 11:27:06.255 [D] gui:718 Add view AmplitudeView to GUI. 11:27:06.256 [D] base:334 Set state for AmplitudeView (1). 11:27:06.273 [D] gui:718 Add view AmplitudeView to GUI. 11:27:06.275 [D] base:334 Set state for AmplitudeView (2). 11:27:06.293 [D] gui:718 Add view AmplitudeView to GUI. 11:27:06.294 [D] base:334 Set state for AmplitudeView (3). 11:27:06.345 [D] gui:718 Add view ProbeView to GUI. 11:27:06.346 [D] base:334 Set state for ProbeView. 11:27:06.358 [D] gui:718 Add view ProbeView to GUI. 11:27:06.359 [D] base:334 Set state for ProbeView (1). 11:27:06.670 [D] gui:519 Load the geometry state.Is anyone else facing this issue.