.command.log - Workdir - DAQ:GERMLINE_CNV:AggregateBatchPerSampleData (HCC1395_BL)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/09/cf942f2230bbeed8ab49ac40fa8998/.command.log
Size: 641.2 KB
Task: DAQ:GERMLINE_CNV:AggregateBatchPerSampleData (HCC1395_BL)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7f/5dfc8ca232417d2e1299914a03a57d/cluster_1387_samples.csv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f7/25ff19bd23e83ddfebf571ef730b18/cluster_1150_samples.csv
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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-2j8i5nnn 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 22:11:58,659 - cnv_pipe.cnv_pipe.batch.agg - INFO - Aggregating data for sample HCC1395_BL
2026-06-03 22:11:58,668 - cnv_pipe.cnv_pipe.batch.agg - INFO - Found 2659 clusters in clusters/
2026-06-03 22:12:05,497 - cnv_pipe.cnv_pipe.batch.agg - INFO - Read model data: 462994 probe-sample rows from 2659 clusters
2026-06-03 22:12:06,027 - cnv_pipe.cnv_pipe.batch.agg - INFO - Read counts: 462994 rows for sample HCC1395_BL
2026-06-03 22:12:06,420 - 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 22:12:07,034 - cnv_pipe.cnv_pipe.batch.agg - INFO - Wrote 462994 rows to HCC1395_BL_probe_sample.parquet