Downloading: s3://natera-platform-sandbox/platform_projects/renasight_cnv/beta_constrain.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d7/98458dae0649ee57628d962f8986b7/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/81/a59045242aff6bbaef7b838b775028/counts_4.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/81/a59045242aff6bbaef7b838b775028/ploidy_4.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6f/318b6d99d402f285c0eaa2b51bc27b/clustered_panel.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/81/a59045242aff6bbaef7b838b775028/sample_metrics_4.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d7/98458dae0649ee57628d962f8986b7/.command.run
==> STAGING COMPLETE (7 inputs)

mkdir -p failed for path /.config/matplotlib: [Errno 13] Permission denied: '/.config'
Matplotlib created a temporary cache directory at /tmp/matplotlib-9yq3ywso because there was an issue with the default path (/.config/matplotlib); it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing.
2026-06-08 23:14:28,762 - cnv_pipe.batch.jax_config - INFO - Setting JAX backend to 'cpu'
2026-06-08 23:14:29,538 - cnv_pipe.batch.run_model - INFO - JAX devices = [CpuDevice(id=0)]
2026-06-08 23:14:29,559 - cnv_pipe.batch.run_model - INFO - Loading counts from counts_4.parquet
2026-06-08 23:14:30,451 - cnv_pipe.batch.run_model - INFO - Loaded data with 93 samples
2026-06-08 23:14:30,452 - cnv_pipe.batch.run_model - INFO - Loading per-probe beta priors from beta_constrain.tsv
2026-06-08 23:14:30,462 - cnv_pipe.batch.run_model - INFO - Matched beta priors for 50 / 22880 probes from beta_constrain.tsv
2026-06-08 23:14:30,846 - cnv_pipe.batch.run_model.cluster90 - INFO - Child process started for cluster 90 with 134 probes
2026-06-08 23:16:57,147 - cnv_pipe.batch.run_model.cluster90 - INFO - Child process finished cluster 90. Wrote clusters_4/cluster_90_samples.csv and clusters_4/cluster_90_params.csv
2026-06-08 23:16:57,149 - cnv_pipe.batch.run_model - INFO - Cluster 90 processed successfully with status SUCCESS
2026-06-08 23:16:57,149 - cnv_pipe.batch.run_model - INFO - All done. Processed the cluster 90 in 146.67 seconds