Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/14/a1202f4232450b378102693f1b89c8/1029_16G-T1-TDNA-1_B23KFCWLT4_1_normalized.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-fd84ed8a-30c3-48a9-9ca6-3c6dc6d33cf1/25/329f810bbfa9ef0c6a909837f14d4a/test_pairs.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1f/882df4bdf23912f4d081f9301ab054/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c4/6979abb33876ff13d137d8146c5679/1029_16G-N1-BDNA-1_B23KGCJLT4_1_normalized.parquet
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ensembl/Homo_sapiens.GRCh38.110.gtf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1f/882df4bdf23912f4d081f9301ab054/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/65/f97729577ec35c74e750264bfde4b6/1029_16G-T1-TDNA-1_B23KFCWLT4_1_alleles.tsv.gz
  Downloading: s3://ai-pipelines-experiment/somatic-cnv/altera_genes_hg38.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a6/d96eb9d3d6e1a44122d4d57fe5f3b5/1029_16G-N1-BDNA-1_B23KGCJLT4_1_alleles.tsv.gz
==> STAGING COMPLETE (9 inputs)

mkdir -p failed for path /.config/matplotlib: [Errno 13] Permission denied: '/.config'
Matplotlib created a temporary cache directory at /tmp/matplotlib-1sqfoc5t 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.
Processing 1 T/N pair(s)...
  Enabled: mode=ascn, joint-seg, purity-estimation, adaptive-pen, weighted-seg, fit=clonal-decomp
  Loading gene annotations from Homo_sapiens.GRCh38.110.gtf.gz...
  Loaded 62062 gene annotations
  [1/1] 1029_16G... MAD=0.2445, pen_mult=1.49  fit_multiclone_select: n_peaks=6, n_segs=219, dipLogR=-0.3760
  Greedy search: 6 model combinations
  n_clones=1 best[0]: sum_rho=0.1595, cost=0.04156, ICL=-1309.59, converged=True, n_iter=3, init=[0.1563], phi=[0.1595]
  n_clones=2 best[0,1]: sum_rho=0.2071, cost=0.03704, ICL=-1320.88, converged=True, n_iter=6, init=[0.1563, 0.1824], phi=[0.1451, 0.0620]
  n_clones=3 best[0,1,2]: sum_rho=0.2629, cost=0.01750, ICL=-1481.78, converged=True, n_iter=17, init=[0.1182, 0.1563, 0.1824], phi=[0.1205, 0.0881, 0.0542]
  n_clones=4 best[0,1,2,3]: sum_rho=0.2717, cost=0.01804, ICL=-1468.11, converged=True, n_iter=9, init=[0.1182, 0.1563, 0.1824, 0.2445], phi=[0.1284, 0.0507, 0.0307, 0.0619]
  n_clones=5 best[0,1,2,3,4]: sum_rho=0.2854, cost=0.01641, ICL=-1484.64, converged=True, n_iter=15, init=[0.0802, 0.1182, 0.1563, 0.1824, 0.2445], phi=[0.0915, 0.0459, 0.0534, 0.0295, 0.0651]
  n_clones=6 best[0,1,2,3,4,5]: sum_rho=0.2869, cost=0.01621, ICL=-1481.89, converged=True, n_iter=16, init=[0.0802, 0.1182, 0.1563, 0.1824, 0.2024, 0.2445], phi=[0.0853, 0.0410, 0.0481, 0.0351, 0.0253, 0.0521]
  SELECTED (best-ICL): n_clones=5, ICL=-1484.64, purity=0.2854 (6 models evaluated)
 219 segments, 219 events, 21083 genes
Wrote 219 segments (219 events) to 1029_16G_segments.tsv
Wrote 1 metrics rows to 1029_16G_metrics.tsv
Wrote 21083 gene entries to 1029_16G_gene_cnv.tsv.gz
Wrote somatic VCF to 1029_16G_somatic.vcf

Single-sample analysis...
  1029_16G (tumor)...  fit_multiclone_select: n_peaks=6, n_segs=303, dipLogR=-0.3660
  Greedy search: 6 model combinations
  n_clones=1 best[0]: sum_rho=0.2081, cost=0.05643, ICL=-1843.98, converged=True, n_iter=6, init=[0.1904], phi=[0.2081]
  n_clones=2 best[0,1]: sum_rho=0.2198, cost=0.03560, ICL=-1945.28, converged=True, n_iter=6, init=[0.1122, 0.1904], phi=[0.1383, 0.0815]
  n_clones=3 best[0,1,2]: sum_rho=0.2629, cost=0.02147, ICL=-2092.35, converged=True, n_iter=29, init=[0.1122, 0.1623, 0.1904], phi=[0.1434, 0.0780, 0.0415]
  n_clones=4 best[0,1,2,3]: sum_rho=0.2845, cost=0.01709, ICL=-2156.02, converged=True, n_iter=28, init=[0.1122, 0.1383, 0.1623, 0.1904], phi=[0.1349, 0.0490, 0.0313, 0.0693]
  n_clones=5 best[0,1,2,3,4]: sum_rho=0.2851, cost=0.02012, ICL=-2099.82, converged=True, n_iter=17, init=[0.1122, 0.1383, 0.1623, 0.1904, 0.2445], phi=[0.1225, 0.0326, 0.0240, 0.0452, 0.0609]
  n_clones=6 best[0,1,2,3,4,5]: sum_rho=0.2920, cost=0.01973, ICL=-2101.43, converged=True, n_iter=24, init=[0.0762, 0.1122, 0.1383, 0.1623, 0.1904, 0.2445], phi=[0.0858, 0.0501, 0.0300, 0.0244, 0.0429, 0.0588]
  SELECTED (best-ICL): n_clones=4, ICL=-2156.02, purity=0.2845 (6 models evaluated)
 303 segments, 303 events
  1029_16G (blood)... 86 segments, 24 events
Single-sample analysis complete.