Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/54/7cbb3a2229435604b24a76b46ac3af/counts_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/54/7cbb3a2229435604b24a76b46ac3af/ploidy_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/df/8ee81d6b6b4fcd312c228fa48d406e/clustered_panel.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/54/7cbb3a2229435604b24a76b46ac3af/sample_metrics_1.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e1/e02e30819308599c89483fea228c84/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e1/e02e30819308599c89483fea228c84/.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-f36vjpho 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.
2026-06-04 16:58:57,452 - cnv_pipe.batch.jax_config - INFO - Setting JAX backend to 'cpu'
2026-06-04 16:58:58,291 - cnv_pipe.batch.run_model - INFO - JAX devices = [CpuDevice(id=0)]
2026-06-04 16:58:58,459 - cnv_pipe.batch.run_model - INFO - Loading counts from counts_1.parquet
2026-06-04 16:58:59,442 - cnv_pipe.batch.run_model - INFO - Loaded data with 4 samples
2026-06-04 16:58:59,519 - cnv_pipe.batch.run_model - INFO - Processing cluster 558 with 190 probes
2026-06-04 16:59:00,005 - cnv_pipe.batch.run_model.cluster558 - INFO - Child process started for cluster 558 with 190 probes
2026-06-04 16:59:56,094 - cnv_pipe.batch.run_model.cluster558 - INFO - Child process finished cluster 558. Wrote cluster_558_samples.csv and cluster_558_params.csv
2026-06-04 16:59:56,095 - cnv_pipe.batch.run_model - INFO - Cluster 558 finished in 56.58 seconds. Status: SUCCESS