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==> 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-v5p3t8ro 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 10:11:10,924 - cnv_pipe.cnv_pipe.batch.agg - INFO - Aggregating data for sample 1029_3HC-N1-BDNA-1_B23K7JFLT3_1
2026-06-03 10:11:10,931 - cnv_pipe.cnv_pipe.batch.agg - INFO - Found 2659 clusters in clusters/
2026-06-03 10:13:03,649 - cnv_pipe.cnv_pipe.batch.agg - INFO - Read model data: 462994 probe-sample rows from 2659 clusters
2026-06-03 10:13:19,991 - cnv_pipe.cnv_pipe.batch.agg - INFO - Read counts: 462994 rows for sample 1029_3HC-N1-BDNA-1_B23K7JFLT3_1
2026-06-03 10:13:20,480 - 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}
2026-06-03 10:13:21,182 - cnv_pipe.cnv_pipe.batch.agg - INFO - Wrote 462994 rows to 1029_3HC-N1-BDNA-1_B23K7JFLT3_1_probe_sample.parquet