Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/83/b1c338b90941ca65375a9bb0d005e0/HCC1395_BL_normalized.parquet Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7e/e7e8b8200e4c7aa496e6b1b175df19/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/57/e4abd07fb24f22d8e8f04917fc8454/HCC1395_BL_alleles.tsv.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/tmp/dc/b7647d544e831e157a3c20bca634c8/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/04/8ba6334d9337bca5f405c4a84ebf3d/HCC1395_tumor_alleles.tsv.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3d/5e12bb7777028529dfa8a4f8bc7696/HCC1395_tumor_normalized.parquet Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7e/e7e8b8200e4c7aa496e6b1b175df19/.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-vs8e3w3g 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] HCC1395_tumor_vs_HCC1395_BL... MAD=0.1651, pen_mult=0.68/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (4) 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 (4) 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 (4) 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 (4) 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 (4) 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 (4) 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 (4) 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 (4) 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 (4) 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 (4) 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 (4) 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 (4) 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 (4) 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 (4) 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 (4) 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 (4) 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 (4) 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 (4) 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 (4) 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 (4) 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 (4) 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 (4) 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 (4) 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 (4) 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 (4) 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=0.0260 Greedy search: 1 model combinations n_clones=1 best[0]: sum_rho=0.9900, cost=0.73529, ICL=-5.00, converged=True, n_iter=2, init=[0.9970], phi=[0.9900] SELECTED (best-ICL): n_clones=1, ICL=-5.00, purity=0.9900 (1 models evaluated) Wrote 4630 probes to HCC1395_tumor_vs_HCC1395_BL_probe_agg.tsv.gz 4 segments, 2 events, 244 genes Wrote 4 segments (2 events) to HCC1395_tumor_vs_HCC1395_BL_segments.tsv Wrote 4 segments to HCC1395_tumor_vs_HCC1395_BL.seg Wrote 1 metrics rows to HCC1395_tumor_vs_HCC1395_BL_metrics.tsv Wrote 244 gene entries to HCC1395_tumor_vs_HCC1395_BL_gene_cnv.tsv.gz Wrote somatic VCF to HCC1395_tumor_vs_HCC1395_BL_somatic.vcf Single-sample analysis... HCC1395_tumor_vs_HCC1395_BL (tumor).../usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (4) 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 (4) 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 (4) 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 (4) 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 (4) 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 (4) 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 (4) 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 (4) 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 (4) 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 (4) 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 (4) 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 (4) 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 (4) 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 (4) 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 (4) 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 (4) 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 (4) 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 (4) 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 (4) 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 (4) 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 (4) 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 (4) 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 (4) 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 (4) 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 (4) 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=5, dipLogR=0.0300 Greedy search: 1 model combinations n_clones=1 best[0]: sum_rho=0.0779, cost=0.00295, ICL=-24.48, converged=True, n_iter=2, init=[0.1250], phi=[0.0779] SELECTED (best-ICL): n_clones=1, ICL=-24.48, purity=0.0779 (1 models evaluated) 5 segments, 5 events Wrote 5 segments to ./tumor_only/HCC1395_tumor_vs_HCC1395_BL.seg Wrote 4630 probes to ./tumor_only/HCC1395_tumor_vs_HCC1395_BL_probe_agg.tsv.gz HCC1395_tumor_vs_HCC1395_BL (blood)... 1 segments, 0 events Wrote 1 segments to ./blood_only/HCC1395_tumor_vs_HCC1395_BL.seg Wrote 4630 probes to ./blood_only/HCC1395_tumor_vs_HCC1395_BL_probe_agg.tsv.gz Single-sample analysis complete.