Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/80/25b5869070f582cfcdda2a1b3e7df8/counts_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/80/25b5869070f582cfcdda2a1b3e7df8/ploidy_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0c/83a6eb5a9efd76c3cc3115568a186b/clustered_panel.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/80/25b5869070f582cfcdda2a1b3e7df8/sample_metrics_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/65/adb91c32b1a3cdb39ba6dba5859605/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/65/adb91c32b1a3cdb39ba6dba5859605/.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-_h3lsref 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 06:10:33,793 - cnv_pipe.batch.jax_config - INFO - Setting JAX backend to 'cpu'
2026-06-03 06:10:34,688 - cnv_pipe.batch.run_model - INFO - JAX devices = [CpuDevice(id=0)]
2026-06-03 06:10:34,869 - cnv_pipe.batch.run_model - INFO - Loading counts from counts_1.parquet
2026-06-03 06:11:21,394 - cnv_pipe.batch.run_model - INFO - Loaded data with 188 samples
2026-06-03 06:11:21,499 - cnv_pipe.batch.run_model - INFO - Processing cluster 861 with 197 probes
2026-06-03 06:11:21,931 - cnv_pipe.batch.run_model.cluster861 - INFO - Child process started for cluster 861 with 197 probes
2026-06-03 06:16:59,731 - cnv_pipe.batch.run_model.cluster861 - INFO - Child process finished cluster 861. Wrote cluster_861_samples.csv and cluster_861_params.csv
2026-06-03 06:16:59,733 - cnv_pipe.batch.run_model - INFO - Cluster 861 finished in 338.23 seconds. Status: SUCCESS