AttributeError: 'EasyDict' object has no attribute 'sites_initial'

[pc2001]

Hi,

Thanks for making the pipeline available!

I was trying to get started with the pipeline. I have already got the SJ.out.tab files from STAR and my config file looks like:

process: junction: /home/data/PID3412/PID3412.SJ threshold: sites_quality: 3 runs_quality: 5 io: log_scale_histogram: false use_label: true label_file: /home/data/PID3412/annotation/metadata_PID3412.csv truth_column: neuron run_column: cell output_path: /home/data/PID3412/PID3412.results impute: num_iteration: 3 knn: 5 cluster: pca_dimension: 20 dimension_reduction_method: umap cluster_algorithm: spectral num_cluster: 3

The SJ.out.tab looks ok. I get the following error:

.. processing junction files: 97%|█████████▋| 221/229 [00:06<00:00, 31.98it/s]^MReading and processing junction files: 98%|█████████▊| 225/229 [00:06<00:00, 33.75it/s]^MReading and processing junction files: 100%|██████████| 229/229 [00:07<00:00, 34.72it/s]^MReading and processing junction files: 100%|██████████| 229/229 [00:07<00:00, 32.60it/s] Traceback (most recent call last): File "/home/programs/SCASL/main.py", line 10, in <module> scasl.fit() File "/beegfs/home/programs/SCASL/scasl/splice.py", line 95, in fit run_cluster(self.cfg) File "/beegfs/home/programs/SCASL/scasl/splice.py", line 54, in run_cluster cfg.threshold.sites_initial, cfg.threshold.runs_initial, AttributeError: 'EasyDict' object has no attribute 'sites_initial'

Do you know where I could be going wrong? Please let me know if there is any other information that I can provide.

Thank you!