Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a9/2c4ec1a4185d8f3025a3f4935fe2e2/HCC1395_BL_normalized.parquet
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/14/9134bf76f5b01069d19766cdb737b3/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a7/0280b7ec3be6b881f06a9e7f99f445/HCC1395_BL_alleles.tsv.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/tmp/8c/98b953b56e4a108fba722e2ef3167e/pairs.tsv
Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/shared/somatic_cnv/Homo_sapiens.GRCh38.110.chr21.gtf.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f2/66c9191e043d9c4a2a17f55972816b/HCC1395_tumor_alleles.tsv.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/03/3f811dc06f0a1ffa0a39177db92082/HCC1395_tumor_normalized.parquet
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/14/9134bf76f5b01069d19766cdb737b3/.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-jr1neos8 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=0.1851, pen_mult=0.86/usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (6) 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 (6) 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 (6) 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 (6) 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 (6) 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 (6) 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 (6) 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 (6) 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 (6) 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 (6) 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 (6) 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 (6) 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 (6) 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 (6) 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 (6) 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 (6) 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 (6) 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 (6) 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 (6) 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 (6) 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 (6) 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 (6) 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 (6) 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 (6) 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 (6) 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=6, dipLogR=0.0300
Greedy search: 1 model combinations
n_clones=1 best[0]: sum_rho=0.0749, cost=0.00108, ICL=-37.27, converged=True, n_iter=2, init=[0.0725], phi=[0.0749]
SELECTED (best-ICL): n_clones=1, ICL=-37.27, purity=0.0749 (1 models evaluated)
Wrote 4580 probes to HCC1395_tumor_vs_HCC1395_BL_probe_agg.tsv.gz
6 segments, 6 events, 246 genes
Wrote 6 segments (6 events) to HCC1395_tumor_vs_HCC1395_BL_segments.tsv
Wrote 6 segments to HCC1395_tumor_vs_HCC1395_BL.seg
Wrote 1 metrics rows to HCC1395_tumor_vs_HCC1395_BL_metrics.tsv
Wrote 246 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 (9) 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 (9) 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 (9) 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 (9) 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 (9) 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 (9) 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 (9) 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 (9) 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 (9) 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 (9) 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 (9) 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 (9) 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 (9) 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 (9) 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 (9) 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 (9) 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 (9) 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 (9) 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 (9) 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 (9) 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 (9) 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 (9) 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 (9) 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 (9) 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 (9) 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=9, dipLogR=0.0300
Greedy search: 1 model combinations
n_clones=1 best[0]: sum_rho=0.9900, cost=2.11429, ICL=-9.88, converged=True, n_iter=2, init=[0.9970], phi=[0.9900]
SELECTED (best-ICL): n_clones=1, ICL=-9.88, purity=0.9900 (1 models evaluated)
9 segments, 5 events
Wrote 9 segments to ./tumor_only/HCC1395_tumor_vs_HCC1395_BL.seg
Wrote 4580 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 4580 probes to ./blood_only/HCC1395_tumor_vs_HCC1395_BL_probe_agg.tsv.gz
Traceback (most recent call last):
File "/usr/local/bin/call_cnv.py", line 2215, in <module>
main()
File "/usr/local/bin/call_cnv.py", line 2171, in main
generate_plots(f"{specimen_id}_{sample_type}",
File "/usr/local/bin/plot_clonal_decomp.py", line 766, in generate_plots
_plot_cost_curve(fit_result, specimen_id, ax_cost)
File "/usr/local/bin/plot_clonal_decomp.py", line 79, in _plot_cost_curve
fold_min = fold_cost_curves.min(axis=0)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/numpy/_core/_methods.py", line 45, in _amin
return umr_minimum(a, axis, None, out, keepdims, initial, where)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ValueError: zero-size array to reduction operation minimum which has no identity