Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/db/a29eebd4a40aa7c28dccf84364dc42/counts_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/db/a29eebd4a40aa7c28dccf84364dc42/ploidy_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/be/5144ad9e68402ab9f76dba7152c49a/clustered_panel.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/db/a29eebd4a40aa7c28dccf84364dc42/sample_metrics_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0f/3aaf9ea5c92091989b47e25aa11d88/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0f/3aaf9ea5c92091989b47e25aa11d88/.command.run
==> STAGING COMPLETE (6 inputs)

mkdir -p failed for path /.config/matplotlib: [Errno 13] Permission denied: '/.config'
Matplotlib created a temporary cache directory at /tmp/matplotlib-bp7a3byg 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.
2026-06-03 04:43:23,072 - cnv_pipe.batch.jax_config - INFO - Setting JAX backend to 'cpu'
2026-06-03 04:43:24,390 - cnv_pipe.batch.run_model - INFO - JAX devices = [CpuDevice(id=0)]
2026-06-03 04:43:24,607 - cnv_pipe.batch.run_model - INFO - Loading counts from counts_1.parquet
2026-06-03 04:43:43,398 - cnv_pipe.batch.run_model - INFO - Loaded data with 72 samples
2026-06-03 04:43:43,781 - cnv_pipe.batch.run_model - INFO - Processing cluster 1040 with 153 probes
2026-06-03 04:43:44,357 - cnv_pipe.batch.run_model.cluster1040 - INFO - Child process started for cluster 1040 with 153 probes
2026-06-03 04:46:30,251 - cnv_pipe.batch.run_model.cluster1040 - INFO - Child process finished cluster 1040. Wrote cluster_1040_samples.csv and cluster_1040_params.csv
2026-06-03 04:46:30,253 - cnv_pipe.batch.run_model - INFO - Cluster 1040 finished in 166.47 seconds. Status: SUCCESS