Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9e/a1781145af4027ce60ad5126c54276/1029_0W2-N1-BDNA-1_B23KGCJLT4_1_normalized.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-02f6c14b-6a09-4281-a8fa-f6a36499687f/ad/a3f996b40cf1f958af55481d7b613c/test_pairs.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f1/5a048c8e4be69911c9c696b60e0580/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2a/5d35da14ba8ddc0a43438b8c726797/1029_0W2-T1-TDNA-1_A23KCGYLT4_1_alleles.tsv.gz
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ensembl/Homo_sapiens.GRCh38.110.gtf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f1/5a048c8e4be69911c9c696b60e0580/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/b347ec8f61f4a2a74a6ba42cfe0cf3/1029_0W2-N1-BDNA-1_B23KGCJLT4_1_alleles.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f0/274b1dd9d676f7e446c208424645cf/1029_0W2-T1-TDNA-1_A23KCGYLT4_1_normalized.parquet
  Downloading: s3://ai-pipelines-experiment/somatic-cnv/altera_genes_hg38.bed
==> 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-swunx30p 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_0W2... MAD=0.2780, pen_mult=1.93  fit_multiclone_select: n_peaks=7, n_segs=210, dipLogR=-0.1960
  Greedy search: 7 model combinations
  n_clones=1 best[0]: sum_rho=0.3551, cost=0.03816, ICL=-1347.05, converged=True, n_iter=3, init=[0.3667], phi=[0.3551]
  n_clones=2 best[0,1]: sum_rho=0.3588, cost=0.01888, ICL=-1439.69, converged=True, n_iter=3, init=[0.0982, 0.3667], phi=[0.0997, 0.2591]
  n_clones=3 best[0,1,2]: sum_rho=0.3609, cost=0.01500, ICL=-1476.39, converged=True, n_iter=7, init=[0.0982, 0.1964, 0.3667], phi=[0.0757, 0.1183, 0.1669]
  n_clones=4 best[0,1,2,3]: sum_rho=0.3693, cost=0.01189, ICL=-1517.63, converged=True, n_iter=10, init=[0.0982, 0.1964, 0.3307, 0.3667], phi=[0.0825, 0.1053, 0.1491, 0.0324]
  n_clones=5 best[0,1,2,3,4]: sum_rho=0.3873, cost=0.00974, ICL=-1554.54, converged=True, n_iter=14, init=[0.0982, 0.1563, 0.1964, 0.3307, 0.3667], phi=[0.1210, 0.0552, 0.0436, 0.1406, 0.0268]
  n_clones=6 best[0,1,2,3,4,5]: sum_rho=0.3898, cost=0.00951, ICL=-1554.81, converged=True, n_iter=27, init=[0.0982, 0.1563, 0.1964, 0.2906, 0.3307, 0.3667], phi=[0.1139, 0.0551, 0.0488, 0.1086, 0.0374, 0.0260]
  n_clones=7 best[0,1,2,3,4,5,6]: sum_rho=0.3930, cost=0.00942, ICL=-1551.95, converged=True, n_iter=10, init=[0.0982, 0.1563, 0.1964, 0.2906, 0.3307, 0.3667, 0.3988], phi=[0.1000, 0.0542, 0.0388, 0.0978, 0.0442, 0.0332, 0.0248]
  SELECTED (best-ICL): n_clones=6, ICL=-1554.81, purity=0.3898 (7 models evaluated)
 210 segments, 210 events, 21083 genes
Wrote 210 segments (210 events) to 1029_0W2_segments.tsv
Wrote 1 metrics rows to 1029_0W2_metrics.tsv
Wrote 21083 gene entries to 1029_0W2_gene_cnv.tsv.gz
Wrote somatic VCF to 1029_0W2_somatic.vcf

Single-sample analysis...
  1029_0W2 (tumor)...  fit_multiclone_select: n_peaks=5, n_segs=270, dipLogR=-0.1920
  Greedy search: 5 model combinations
  n_clones=1 best[0]: sum_rho=0.3568, cost=0.04707, ICL=-1744.61, converged=True, n_iter=2, init=[0.3667], phi=[0.3568]
  n_clones=2 best[0,1]: sum_rho=0.3645, cost=0.02343, ICL=-1856.80, converged=True, n_iter=4, init=[0.1142, 0.3667], phi=[0.1027, 0.2618]
  n_clones=3 best[0,1,2]: sum_rho=0.3667, cost=0.01764, ICL=-1919.47, converged=True, n_iter=7, init=[0.1142, 0.3206, 0.3667], phi=[0.1131, 0.1977, 0.0560]
  n_clones=4 best[0,1,2,3]: sum_rho=0.3783, cost=0.01402, ICL=-1974.78, converged=True, n_iter=9, init=[0.1142, 0.1784, 0.3206, 0.3667], phi=[0.1240, 0.0745, 0.1476, 0.0322]
  n_clones=5 best[0,1,2,3,4]: sum_rho=0.3786, cost=0.01362, ICL=-1976.69, converged=True, n_iter=15, init=[0.1142, 0.1784, 0.2625, 0.3206, 0.3667], phi=[0.1169, 0.0780, 0.0972, 0.0567, 0.0299]
  SELECTED (best-ICL): n_clones=5, ICL=-1976.69, purity=0.3786 (5 models evaluated)
 270 segments, 269 events
  1029_0W2 (blood)... 184 segments, 81 events
Single-sample analysis complete.