Error executing process > 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:SOMATIC_CNV_CALLING:SOMA_CNV_CALL (HCC1395_tumor_vs_HCC1395_BL)'

Caused by:
  Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:SOMATIC_CNV_CALLING:SOMA_CNV_CALL (HCC1395_tumor_vs_HCC1395_BL)` terminated with an error exit status (1)


Command executed:

  python /usr/local/bin/call_cnv.py \
      --tumor-parquet HCC1395_tumor_normalized.parquet \
      --normal-parquet HCC1395_BL_normalized.parquet \
      --pairs pairs.tsv \
      --specimen HCC1395_tumor_vs_HCC1395_BL \
      --output HCC1395_tumor_vs_HCC1395_BL_segments.tsv \
      --seg-output HCC1395_tumor_vs_HCC1395_BL.seg \
      --tumor-alleles HCC1395_tumor_alleles.tsv.gz \
      --normal-alleles HCC1395_BL_alleles.tsv.gz \
      --probe-agg-output HCC1395_tumor_vs_HCC1395_BL_probe_agg.tsv.gz \
      --plots-dir plots \
      --metrics-output HCC1395_tumor_vs_HCC1395_BL_metrics.tsv \
      --workers 4 \
       \
      --genome-annotations Homo_sapiens.GRCh38.110.chr21.gtf.gz \
      --gene-output HCC1395_tumor_vs_HCC1395_BL_gene_cnv.tsv \
      --vcf-output HCC1395_tumor_vs_HCC1395_BL_somatic.vcf \
      --fit-method clonal-decomp --mode ascn
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:SOMATIC_CNV_CALLING:SOMA_CNV_CALL":
      soma-cnv: 20260604-fbf83cd
  END_VERSIONS

Command exit status:
  1

Command output:
  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  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)...  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

Command error:
  /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)
  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

Work dir:
  s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1a/c128e14e0ee2458b7a1449fc3a3406

Container:
  292967571998.dkr.ecr.us-west-2.amazonaws.com/soma-cnv:20260604-fbf83cd

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`