Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta
  Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/shared/germline_cnv_model.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e5/c46c112cbf5e1c9dde5af7c9d06f11/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e5/c46c112cbf5e1c9dde5af7c9d06f11/.command.run
==> STAGING COMPLETE (4 inputs)

mkdir -p failed for path /.config/matplotlib: [Errno 13] Permission denied: '/.config'
Matplotlib created a temporary cache directory at /tmp/matplotlib-ux_2551t 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 19:31:54,433 - cnv_pipe.cnv_pipe.batch.probe_merger - INFO - Resolved panel_conf 'altera' to bundled /opt/venv/lib/python3.12/site-packages/cnv_pipe/conf/altera.conf
2026-06-04 19:31:54,434 - cnv_pipe.cnv_pipe.batch.probe_merger - INFO - Loaded panel_conf from /opt/venv/lib/python3.12/site-packages/cnv_pipe/conf/altera.conf: LOW_CONF_Z=2.0 HIGH_CONF_Z=5.0 HMM_WEIGHT=5.0 HIGHCONF_BOUNDS=(-17.0,11.0) LOWCONF_BOUNDS=(-7.0,5.0)
2026-06-04 19:31:54,434 - cnv_pipe.cnv_pipe.batch.probe_merger - INFO - Reading input file: germline_cnv_model.parquet
2026-06-04 19:31:54,471 - cnv_pipe.cnv_pipe.batch.probe_merger - INFO - Reading reference genome FASTA file: Homo_sapiens_assembly38.fasta
2026-06-04 19:32:02,018 - cnv_pipe.cnv_pipe.batch.probe_merger - INFO - Filtered out 1218 probes with mask flags (mask_probes_low, mask_probes_blacklist)
2026-06-04 19:32:02,018 - cnv_pipe.cnv_pipe.batch.probe_merger - INFO - Failed probes (mask_probes_low or mask_probe_model_failed): 2
2026-06-04 19:32:02,018 - cnv_pipe.cnv_pipe.batch.probe_merger - INFO - Remaining probes: 56446
2026-06-04 19:32:02,019 - cnv_pipe.cnv_pipe.batch.probe_merger - INFO - Single sample — skipping batch FC statistics
2026-06-04 19:32:02,019 - cnv_pipe.cnv_pipe.batch.probe_merger - INFO - Processing 1 samples with 1 threads
2026-06-04 19:32:03,508 - cnv_pipe.cnv_pipe.batch.probe_merger - INFO - Processed 3574109522_sv1: 2 deletions, 0 duplications
2026-06-04 19:32:03,508 - cnv_pipe.cnv_pipe.batch.probe_merger - INFO - 
Processing complete!
2026-06-04 19:32:03,508 - cnv_pipe.cnv_pipe.batch.probe_merger - INFO - Total samples successfully processed: 1
2026-06-04 19:32:03,508 - cnv_pipe.cnv_pipe.batch.probe_merger - INFO - Number of samples failed QC: 0
2026-06-04 19:32:03,508 - cnv_pipe.cnv_pipe.batch.probe_merger - INFO - Number of probes failed QC: 2
2026-06-04 19:32:03,508 - cnv_pipe.cnv_pipe.batch.probe_merger - INFO - Total deletions: 2
2026-06-04 19:32:03,508 - cnv_pipe.cnv_pipe.batch.probe_merger - INFO - Total duplications: 0