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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-z7yov858 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 15:51:43,962 - cnv_pipe.cnv_pipe.batch.agg - INFO - Aggregating data for sample HCC1395_tumor
2026-05-27 15:51:43,973 - cnv_pipe.cnv_pipe.batch.agg - INFO - Found 2659 clusters in clusters/
2026-05-27 15:51:52,367 - cnv_pipe.cnv_pipe.batch.agg - INFO - Read model data: 462994 probe-sample rows from 2659 clusters
2026-05-27 15:51:52,919 - cnv_pipe.cnv_pipe.batch.agg - INFO - Read counts: 462994 rows for sample HCC1395_tumor
2026-05-27 15:51:53,355 - 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': 4, 'chr9': 0}
2026-05-27 15:51:54,075 - cnv_pipe.cnv_pipe.batch.agg - INFO - Wrote 462994 rows to HCC1395_tumor_probe_sample.parquet