Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a8/a824105a000bd4102efd8aadd86274/counts_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a8/a824105a000bd4102efd8aadd86274/ploidy_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9c/b41f3d5e56a31b4a017a00332debe8/clustered_panel.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a8/a824105a000bd4102efd8aadd86274/sample_metrics_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0d/2c83959ceba6505f9f38112abcdf55/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0d/2c83959ceba6505f9f38112abcdf55/.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-5bs39qkz 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 05:31:53,429 - cnv_pipe.batch.jax_config - INFO - Setting JAX backend to 'cpu'
2026-06-03 05:31:54,376 - cnv_pipe.batch.run_model - INFO - JAX devices = [CpuDevice(id=0)]
2026-06-03 05:31:54,559 - cnv_pipe.batch.run_model - INFO - Loading counts from counts_1.parquet
2026-06-03 05:32:44,032 - cnv_pipe.batch.run_model - INFO - Loaded data with 190 samples
2026-06-03 05:32:44,145 - cnv_pipe.batch.run_model - INFO - Processing cluster 940 with 200 probes
2026-06-03 05:32:44,612 - cnv_pipe.batch.run_model.cluster940 - INFO - Child process started for cluster 940 with 200 probes
2026-06-03 05:38:43,945 - cnv_pipe.batch.run_model.cluster940 - INFO - Child process finished cluster 940. Wrote cluster_940_samples.csv and cluster_940_params.csv
2026-06-03 05:38:43,948 - cnv_pipe.batch.run_model - INFO - Cluster 940 finished in 359.80 seconds. Status: SUCCESS