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/68d1755f65e1dbb972757f579c183b/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0f/68d1755f65e1dbb972757f579c183b/.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-coofswqd 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 04:43:00,746 - cnv_pipe.batch.jax_config - INFO - Setting JAX backend to 'cpu'
2026-06-03 04:43:01,529 - cnv_pipe.batch.run_model - INFO - JAX devices = [CpuDevice(id=0)]
2026-06-03 04:43:01,696 - cnv_pipe.batch.run_model - INFO - Loading counts from counts_1.parquet
2026-06-03 04:43:17,444 - cnv_pipe.batch.run_model - INFO - Loaded data with 72 samples
2026-06-03 04:43:17,669 - cnv_pipe.batch.run_model - INFO - Processing cluster 900 with 181 probes
2026-06-03 04:43:18,047 - cnv_pipe.batch.run_model.cluster900 - INFO - Child process started for cluster 900 with 181 probes
2026-06-03 04:46:42,518 - cnv_pipe.batch.run_model.cluster900 - INFO - Child process finished cluster 900. Wrote cluster_900_samples.csv and cluster_900_params.csv
2026-06-03 04:46:42,520 - cnv_pipe.batch.run_model - INFO - Cluster 900 finished in 204.85 seconds. Status: SUCCESS