Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8a/c7611cfc97f6ded658168c06a3dc2c/counts_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8a/c7611cfc97f6ded658168c06a3dc2c/ploidy_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7e/c6f1a4c7809881b67eefc20778f6dd/clustered_panel.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8a/c7611cfc97f6ded658168c06a3dc2c/sample_metrics_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7d/b9237157ef0d8097a5cfcda3811bf0/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7d/b9237157ef0d8097a5cfcda3811bf0/.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-iaqbutws 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 21:03:29,897 - cnv_pipe.batch.jax_config - INFO - Setting JAX backend to 'cpu'
2026-06-03 21:03:30,679 - cnv_pipe.batch.run_model - INFO - JAX devices = [CpuDevice(id=0)]
2026-06-03 21:03:30,845 - cnv_pipe.batch.run_model - INFO - Loading counts from counts_1.parquet
2026-06-03 21:03:31,722 - cnv_pipe.batch.run_model - INFO - Loaded data with 4 samples
2026-06-03 21:03:31,885 - cnv_pipe.batch.run_model - INFO - Processing cluster 1099 with 197 probes
2026-06-03 21:03:32,250 - cnv_pipe.batch.run_model.cluster1099 - INFO - Child process started for cluster 1099 with 197 probes
2026-06-03 21:04:26,823 - cnv_pipe.batch.run_model.cluster1099 - INFO - Child process finished cluster 1099. Wrote cluster_1099_samples.csv and cluster_1099_params.csv
2026-06-03 21:04:26,824 - cnv_pipe.batch.run_model - INFO - Cluster 1099 finished in 54.94 seconds. Status: SUCCESS