Open mzj0418 opened 10 months ago
Hello!
Thank you for the tool. I am interested in trying this tool on my own data(Stereo-seq data['geneID', 'x', 'y', 'MIDCounts']).
baysor run ./stereo-seq.csv -p -c ./configs/example_config.toml -p -o ./stereo-seq_output_no_dapi/ -m 1 -g 'geneID' -s 8 [17:11:06] Info: Run R1b9f25c4f [17:11:06] Info: (2023-09-15) Run Baysor v0.6.2 [17:11:06] Info: Loading data... [17:11:08] Info: Loaded 138957 transcripts [17:11:10] Info: Estimating noise level [17:11:16] Info: Done [17:11:29] Info: Clustering molecules... Progress: 100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| Time: 0:00:02 Iteration: 66 Max. difference: 9.26e-5 Fraction of probs changed: 0.00238 [17:12:51] Info: Algorithm stopped after 66 iterations. Error: 9.26e-5. Converged: true. [17:12:51] Info: Done [17:12:51] Info: Initializing algorithm. Scale: 8.0, scale std: 2.0, initial #components: 92638, #molecules: 138957. [17:12:51] Warning: n=92638, which is > length(high_conf_ids) (2553) └ Baysor.Processing /home/viktor_petukhov/.julia/dev/Baysor/src/processing/data_processing/initialization.jl:180 [17:12:52] Info: Using the following additional information about molecules: [:confidence, :cluster] [17:12:52] Info: Using 2D coordinates Progress: 100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| Time: 0:03:45 Iteration: 500 Noise level, %: 98.17 Num. components: 319 [17:16:39] Info: Processing complete. [17:16:39] Info: Estimating local colors [17:18:42] Warning: n=10000, which is > length(high_conf_ids) (2553) └ Baysor.Processing /home/viktor_petukhov/.julia/dev/Baysor/src/processing/data_processing/initialization.jl:180 [17:24:19] Info: Estimating boundary polygons [17:24:20] Info: Saving results to ./stereo-seq_output_no_dapi/segmentation.csv Progress: 100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| Time: 0:00:07 [17:24:35] Info: Plotting results [17:24:37] Info: Plot diagnostics [17:24:39] Info: Plot transcript assignment [17:24:46] Info: All done! (process:3486428): GLib-CRITICAL : 17:24:46.069: g_datalist_id_set_data_full: assertion 'key_id > 0' failed (process:3486428): GLib-CRITICAL : 17:24:46.069: g_datalist_id_set_data_full: assertion 'key_id > 0' failed (process:3486428): GLib-CRITICAL **: 17:24:46.070: g_datalist_id_set_data_full: assertion 'key_id > 0' failed
I don't know if this is correct, I looked at the output file "segmentation.csv" and found that the cell column value is NaN, can you help me find this error?
Best, Jun
Hello!
Thank you for the tool. I am interested in trying this tool on my own data(Stereo-seq data['geneID', 'x', 'y', 'MIDCounts']).
baysor run ./stereo-seq.csv -p -c ./configs/example_config.toml -p -o ./stereo-seq_output_no_dapi/ -m 1 -g 'geneID' -s 8 [17:11:06] Info: Run R1b9f25c4f [17:11:06] Info: (2023-09-15) Run Baysor v0.6.2 [17:11:06] Info: Loading data... [17:11:08] Info: Loaded 138957 transcripts [17:11:10] Info: Estimating noise level [17:11:16] Info: Done [17:11:29] Info: Clustering molecules... Progress: 100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| Time: 0:00:02 Iteration: 66 Max. difference: 9.26e-5 Fraction of probs changed: 0.00238 [17:12:51] Info: Algorithm stopped after 66 iterations. Error: 9.26e-5. Converged: true. [17:12:51] Info: Done [17:12:51] Info: Initializing algorithm. Scale: 8.0, scale std: 2.0, initial #components: 92638, #molecules: 138957. [17:12:51] Warning: n=92638, which is > length(high_conf_ids) (2553) └ Baysor.Processing /home/viktor_petukhov/.julia/dev/Baysor/src/processing/data_processing/initialization.jl:180 [17:12:52] Info: Using the following additional information about molecules: [:confidence, :cluster] [17:12:52] Info: Using 2D coordinates Progress: 100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| Time: 0:03:45 Iteration: 500 Noise level, %: 98.17 Num. components: 319 [17:16:39] Info: Processing complete. [17:16:39] Info: Estimating local colors [17:18:42] Warning: n=10000, which is > length(high_conf_ids) (2553) └ Baysor.Processing /home/viktor_petukhov/.julia/dev/Baysor/src/processing/data_processing/initialization.jl:180 [17:24:19] Info: Estimating boundary polygons [17:24:20] Info: Saving results to ./stereo-seq_output_no_dapi/segmentation.csv Progress: 100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| Time: 0:00:07 [17:24:35] Info: Plotting results [17:24:37] Info: Plot diagnostics [17:24:39] Info: Plot transcript assignment [17:24:46] Info: All done! (process:3486428): GLib-CRITICAL : 17:24:46.069: g_datalist_id_set_data_full: assertion 'key_id > 0' failed (process:3486428): GLib-CRITICAL : 17:24:46.069: g_datalist_id_set_data_full: assertion 'key_id > 0' failed (process:3486428): GLib-CRITICAL **: 17:24:46.070: g_datalist_id_set_data_full: assertion 'key_id > 0' failed
I don't know if this is correct, I looked at the output file "segmentation.csv" and found that the cell column value is NaN, can you help me find this error?
Best, Jun