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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-lebfvui3 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 21:28:14,117 - cnv_pipe.cnv_pipe.batch.agg - INFO - Aggregating data for sample HCC1395_BL
2026-06-03 21:28:14,129 - cnv_pipe.cnv_pipe.batch.agg - INFO - Found 2659 clusters in clusters/
2026-06-03 21:28:24,198 - cnv_pipe.cnv_pipe.batch.agg - INFO - Read model data: 462994 probe-sample rows from 2659 clusters
2026-06-03 21:28:24,959 - cnv_pipe.cnv_pipe.batch.agg - INFO - Read counts: 462994 rows for sample HCC1395_BL
2026-06-03 21:28:25,641 - cnv_pipe.cnv_pipe.batch.agg - INFO - Ploidy (sex=ProcessBatch, auto=posteriors): {'chrX': 1, 'chrY': 0, 'chr1': 0, 'chr12': 0, 'chr14': 0, 'chr19': 0, 'chr21': 2, 'chr5': 0, 'chr6': 0, 'chr7': 0, 'chr9': 0}
2026-06-03 21:28:26,708 - cnv_pipe.cnv_pipe.batch.agg - INFO - Wrote 462994 rows to HCC1395_BL_probe_sample.parquet