Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/655a5e8e00442492d221f5536ab6cf/counts_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/655a5e8e00442492d221f5536ab6cf/ploidy_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/80/c3d8bfb7b4fd5305aa317b2ea43fa9/clustered_panel.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/655a5e8e00442492d221f5536ab6cf/sample_metrics_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f9/9a291c4e91f4d659f343a60391d59a/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f9/9a291c4e91f4d659f343a60391d59a/.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-j_wts5p7 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 04:41:05,136 - cnv_pipe.batch.jax_config - INFO - Setting JAX backend to 'cpu'
2026-06-03 04:41:05,947 - cnv_pipe.batch.run_model - INFO - JAX devices = [CpuDevice(id=0)]
2026-06-03 04:41:06,120 - cnv_pipe.batch.run_model - INFO - Loading counts from counts_1.parquet
2026-06-03 04:41:21,843 - cnv_pipe.batch.run_model - INFO - Loaded data with 72 samples
2026-06-03 04:41:21,939 - cnv_pipe.batch.run_model - INFO - Processing cluster 997 with 191 probes
2026-06-03 04:41:22,552 - cnv_pipe.batch.run_model.cluster997 - INFO - Child process started for cluster 997 with 191 probes
2026-06-03 04:44:51,142 - cnv_pipe.batch.run_model.cluster997 - INFO - Child process finished cluster 997. Wrote cluster_997_samples.csv and cluster_997_params.csv
2026-06-03 04:44:51,146 - cnv_pipe.batch.run_model - INFO - Cluster 997 finished in 209.21 seconds. Status: SUCCESS