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: 20260603-050173b
  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)...

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)
  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 2117, in main
      ss_result, ss_probes, ss_clones, ss_metrics = call_cnv_single_sample(
                                                    ^^^^^^^^^^^^^^^^^^^^^^^
    File "/usr/local/bin/call_cnv.py", line 1668, in call_cnv_single_sample
      result_df, clone_summary, metrics = run_germline_decomp(
                                          ^^^^^^^^^^^^^^^^^^^^
    File "/usr/local/bin/clonal_decomp.py", line 1750, in run_germline_decomp
      fit_result = fit_diploid_logr(df, dipLogR_range=germ_dipLogR_range,
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/usr/local/bin/clonal_decomp.py", line 373, in fit_diploid_logr
      fold_cost_curves[fi] = future.result()
                             ^^^^^^^^^^^^^^^
    File "/usr/local/lib/python3.12/concurrent/futures/_base.py", line 449, in result
      return self.__get_result()
             ^^^^^^^^^^^^^^^^^^^
    File "/usr/local/lib/python3.12/concurrent/futures/_base.py", line 401, in __get_result
      raise self._exception
    File "/usr/local/lib/python3.12/concurrent/futures/thread.py", line 59, in run
      result = self.fn(*self.args, **self.kwargs)
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/usr/local/bin/clonal_decomp.py", line 361, in _cv_fold
      return _compute_cost_curve(
             ^^^^^^^^^^^^^^^^^^^^
    File "/usr/local/bin/clonal_decomp.py", line 233, in _compute_cost_curve
      chunk_d = max(1, int(5e8 / (S * C * 8)))
                           ~~~~^~~~~~~~~~~~~
  ZeroDivisionError: float division by zero

Work dir:
  s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b1/cee08170613d4dba8281984985f0b0

Container:
  292967571998.dkr.ecr.us-west-2.amazonaws.com/soma-cnv:20260603-050173b

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`