Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c4/ac6d9512d4af764498a345612eafa3/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/76/65fe7dd8e20e396d37d9c6a93e0cc7/Sig_18_tissue_alleles.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5b/6990f4e3294c23f58d11e1095328e1/Sig_18_Blood_alleles.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/03/dcd70f59c8cc1098854a530e2f9922/Sig_18_Blood_normalized.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/tmp/c8/89efe95e63f6cc930ec7df6fee5bf7/pairs.tsv
  Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/somatic_cnv/Homo_sapiens.GRCh38.110.chr21.gtf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fd/9def3be944f50c9b8785b927d0ad6e/Sig_18_tissue_normalized.parquet
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c4/ac6d9512d4af764498a345612eafa3/.command.run
==> STAGING COMPLETE (8 inputs)

mkdir -p failed for path /.config/matplotlib: [Errno 13] Permission denied: '/.config'
Matplotlib created a temporary cache directory at /tmp/matplotlib-woxfwck_ 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.chr21.gtf.gz...
  Loaded 898 gene annotations
  [1/1] custom_Sig_18_tumor_normal... MAD=0.2360, pen_mult=1.39/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (3) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (3) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (3) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (3) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (3) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (3) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (3) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (3) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (3) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (3) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (3) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (3) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (3) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (3) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (3) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (3) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (3) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (3) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (3) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (3) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (3) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (3) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (3) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (3) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (3) found smaller than n_clusters (12). Possibly due to duplicate points in X.
  return fit_method(estimator, *args, **kwargs)
  fit_multiclone_select: n_peaks=1, n_segs=4, dipLogR=-0.0240
  Greedy search: 1 model combinations
  n_clones=1 best[0]: sum_rho=0.0815, cost=0.00233, ICL=-17.42, converged=True, n_iter=2, init=[0.0773], phi=[0.0815]
  SELECTED (best-ICL): n_clones=1, ICL=-17.42, purity=0.0815 (1 models evaluated)
Wrote 4632 probes to custom_Sig_18_tumor_normal_probe_agg.tsv.gz
 4 segments, 4 events, 246 genes
Wrote 4 segments (4 events) to custom_Sig_18_tumor_normal_segments.tsv
Wrote 4 segments to custom_Sig_18_tumor_normal.seg
Wrote 1 metrics rows to custom_Sig_18_tumor_normal_metrics.tsv
Wrote 246 gene entries to custom_Sig_18_tumor_normal_gene_cnv.tsv.gz
Wrote somatic VCF to custom_Sig_18_tumor_normal_somatic.vcf

Single-sample analysis...
  custom_Sig_18_tumor_normal (tumor)...  fit_multiclone_select: n_peaks=2, n_segs=15, dipLogR=-0.0620
  Greedy search: 2 model combinations
  n_clones=1 best[0]: sum_rho=0.0377, cost=0.00362, ICL=-81.19, converged=True, n_iter=3, init=[0.0344], phi=[0.0377]
  n_clones=2 best[0,1]: sum_rho=0.1639, cost=0.00344, ICL=-80.93, converged=True, n_iter=5, init=[0.0344, 0.0882], phi=[0.0377, 0.1261]
  SELECTED (best-ICL): n_clones=1, ICL=-81.19, purity=0.0377 (2 models evaluated)
 15 segments, 15 events
Wrote 15 segments to ./tumor_only/custom_Sig_18_tumor_normal.seg
Wrote 4632 probes to ./tumor_only/custom_Sig_18_tumor_normal_probe_agg.tsv.gz
  custom_Sig_18_tumor_normal (blood)... 7 segments, 3 events
Wrote 7 segments to ./blood_only/custom_Sig_18_tumor_normal.seg
Wrote 4632 probes to ./blood_only/custom_Sig_18_tumor_normal_probe_agg.tsv.gz
Single-sample analysis complete.