Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c3/a89dc653765d7ca362153a7e7ec24f/1029_11H-T1-TDNA-1_B23KFCWLT4_1_alleles.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-ebcc93d4-e9ea-47eb-b30f-59cd345a3020/8e/4b5b28637bd021a53190619e56a2db/test_pairs.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4e/5ea0ba9d5591dab753d53dfe6297c4/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b0/16dd3952423ea959501215e4ea8883/1029_11H-T1-TDNA-1_B23KFCWLT4_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/4e/5ea0ba9d5591dab753d53dfe6297c4/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a5/ef184b087643169d7c4df9f4facad4/1029_11H-N1-BDNA-1_B23KGCJLT4_1_normalized.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bd/ba9acdb356e2057e7eb6c81c2831d1/1029_11H-N1-BDNA-1_B23KGCJLT4_1_alleles.tsv.gz
  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-__voat9k 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_11H... MAD=0.3773, pen_mult=3.56  fit_multiclone_select: n_peaks=6, n_segs=189, dipLogR=0.2580
  Greedy search: 6 model combinations
  n_clones=1 best[0]: sum_rho=0.8096, cost=0.43940, ICL=-1054.48, converged=True, n_iter=3, init=[0.8277], phi=[0.8096]
  n_clones=2 best[0,1]: sum_rho=0.8108, cost=0.06092, ICL=-1308.45, converged=True, n_iter=3, init=[0.3968, 0.8277], phi=[0.3789, 0.4318]
  n_clones=3 best[0,1,2]: sum_rho=0.8176, cost=0.02887, ICL=-1403.18, converged=True, n_iter=4, init=[0.3968, 0.7776, 0.8277], phi=[0.4048, 0.3683, 0.0444]
  n_clones=4 best[0,1,2,3]: sum_rho=0.8176, cost=0.02407, ICL=-1423.97, converged=True, n_iter=4, init=[0.1443, 0.3968, 0.7776, 0.8277], phi=[0.1151, 0.2867, 0.3764, 0.0394]
  n_clones=5 best[0,1,2,3,4]: sum_rho=0.8773, cost=0.02236, ICL=-1435.21, converged=True, n_iter=8, init=[0.1443, 0.3968, 0.7776, 0.8277, 0.8798], phi=[0.1210, 0.2761, 0.3849, 0.0350, 0.0603]
  n_clones=6 best[0,1,2,3,4,5]: sum_rho=0.8797, cost=0.02265, ICL=-1427.12, converged=True, n_iter=9, init=[0.1443, 0.3968, 0.6273, 0.7776, 0.8277, 0.8798], phi=[0.1391, 0.2551, 0.2264, 0.1591, 0.0372, 0.0628]
  SELECTED (best-ICL): n_clones=5, ICL=-1435.21, purity=0.8773 (6 models evaluated)
Wrote 435562 probes to 1029_11H_probe_agg.tsv.gz
 189 segments, 189 events, 21100 genes
Wrote 189 segments (189 events) to 1029_11H_segments.tsv
Wrote 1 metrics rows to 1029_11H_metrics.tsv
Wrote 21100 gene entries to 1029_11H_gene_cnv.tsv.gz
Wrote somatic VCF to 1029_11H_somatic.vcf

Single-sample analysis...
  1029_11H (tumor)...  fit_multiclone_select: n_peaks=5, n_segs=194, dipLogR=0.2580
  Greedy search: 5 model combinations
  n_clones=1 best[0]: sum_rho=0.8052, cost=0.44100, ICL=-1092.82, converged=True, n_iter=2, init=[0.8297], phi=[0.8052]
  n_clones=2 best[0,1]: sum_rho=0.8055, cost=0.07633, ICL=-1312.84, converged=True, n_iter=3, init=[0.4108, 0.8297], phi=[0.3747, 0.4308]
  n_clones=3 best[0,1,2]: sum_rho=0.8108, cost=0.03147, ICL=-1437.53, converged=True, n_iter=6, init=[0.1543, 0.4108, 0.8297], phi=[0.0691, 0.3152, 0.4266]
  n_clones=4 best[0,1,2,3]: sum_rho=0.8175, cost=0.02258, ICL=-1488.49, converged=True, n_iter=19, init=[0.1543, 0.4108, 0.7275, 0.8297], phi=[0.0816, 0.3167, 0.3839, 0.0354]
  n_clones=5 best[0,1,2,3,4]: sum_rho=0.8174, cost=0.02200, ICL=-1484.73, converged=True, n_iter=16, init=[0.1543, 0.4108, 0.5691, 0.7275, 0.8297], phi=[0.0814, 0.3162, 0.1822, 0.2022, 0.0354]
  SELECTED (best-ICL): n_clones=4, ICL=-1488.49, purity=0.8175 (5 models evaluated)
 194 segments, 194 events
Wrote 435562 probes to ./tumor_only/1029_11H_probe_agg.tsv.gz
  1029_11H (blood)... 121 segments, 43 events
Wrote 435562 probes to ./blood_only/1029_11H_probe_agg.tsv.gz
Single-sample analysis complete.