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Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/70/e09daaf8204d17ad333bac5af482b0/cluster_659_samples.csv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/67/12c53bbdbee1883bee2e940780eafa/cluster_1548_params.csv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ec/f0b2f13511881a7b9e749abcfd9306/cluster_2209_samples.csv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2d/b7cf3d7e363af84e2800f67865c170/cluster_2581_samples.csv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/28/f56f430f947f037c8c94b55cf6aeb2/cluster_1060_samples.csv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/10/5128af8905bf18703ff0857487caab/cluster_876_samples.csv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2a/9dd112ab93d5fccba5ee9f0c3394a0/cluster_1977_params.csv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/39/56dd06bbcf4686304092866872dd50/cluster_366_samples.csv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9d/8bcf525413765e72514543fe7f5224/cluster_884_params.csv
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Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/47/10b949655cd2c5fee878d297049a03/cluster_851_samples.csv
==> STAGING COMPLETE (5325 inputs)
mkdir -p failed for path /.config/matplotlib: [Errno 13] Permission denied: '/.config'
Matplotlib created a temporary cache directory at /tmp/matplotlib-83a4dnmf 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.
2026-05-27 19:34:03,989 - cnv_pipe.cnv_pipe.batch.agg - INFO - Aggregating data for sample 1029_QZ1-N1-BDNA-1_B23KFG5LT4_1
2026-05-27 19:34:03,999 - cnv_pipe.cnv_pipe.batch.agg - INFO - Found 2659 clusters in clusters/
2026-05-27 19:36:30,685 - cnv_pipe.cnv_pipe.batch.agg - INFO - Read model data: 462994 probe-sample rows from 2659 clusters
2026-05-27 19:36:49,440 - cnv_pipe.cnv_pipe.batch.agg - INFO - Read counts: 462994 rows for sample 1029_QZ1-N1-BDNA-1_B23KFG5LT4_1
2026-05-27 19:36:50,194 - cnv_pipe.cnv_pipe.batch.agg - INFO - Ploidy (sex=ProcessBatch, auto=posteriors): {'chrX': 1, 'chrY': 1, 'chr1': 2, 'chr10': 2, 'chr11': 2, 'chr12': 2, 'chr13': 2, 'chr14': 2, 'chr15': 2, 'chr16': 2, 'chr17': 2, 'chr18': 2, 'chr19': 2, 'chr2': 2, 'chr20': 2, 'chr21': 2, 'chr22': 2, 'chr3': 2, 'chr4': 2, 'chr5': 2, 'chr6': 2, 'chr7': 2, 'chr8': 2, 'chr9': 2}
2026-05-27 19:36:51,293 - cnv_pipe.cnv_pipe.batch.agg - INFO - Wrote 462994 rows to 1029_QZ1-N1-BDNA-1_B23KFG5LT4_1_probe_sample.parquet