Error executing process > 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:SOMATIC_CNV_CALLING:SOMA_CNV_CALL (custom_Sig_18_tumor_normal)'

Caused by:
  Process `NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:SOMATIC_CNV_CALLING:SOMA_CNV_CALL (custom_Sig_18_tumor_normal)` terminated with an error exit status (1)


Command executed:

  python /usr/local/bin/call_cnv.py \
      --tumor-parquet Sig_18_tissue_normalized.parquet \
      --normal-parquet Sig_18_Blood_normalized.parquet \
      --pairs pairs.tsv \
      --specimen custom_Sig_18_tumor_normal \
      --output custom_Sig_18_tumor_normal_segments.tsv \
      --seg-output custom_Sig_18_tumor_normal.seg \
      --tumor-alleles Sig_18_tissue_alleles.tsv.gz \
      --normal-alleles Sig_18_Blood_alleles.tsv.gz \
      --probe-agg-output custom_Sig_18_tumor_normal_probe_agg.tsv.gz \
      --plots-dir plots \
      --metrics-output custom_Sig_18_tumor_normal_metrics.tsv \
      --workers 4 \
       \
      --genome-annotations Homo_sapiens.GRCh38.110.chr21.gtf.gz \
      --gene-output custom_Sig_18_tumor_normal_gene_cnv.tsv \
      --vcf-output custom_Sig_18_tumor_normal_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: 20260604-9c39aac
  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] custom_Sig_18_tumor_normal... MAD=0.2363, pen_mult=1.40  fit_multiclone_select: n_peaks=4, n_segs=13, dipLogR=-0.1080
    Greedy search: 4 model combinations
    n_clones=1 best[0]: sum_rho=0.2016, cost=0.12318, ICL=-29.15, converged=True, n_iter=2, init=[0.2156], phi=[0.2016]
    n_clones=2 best[0,1]: sum_rho=0.2159, cost=0.01157, ICL=-52.39, converged=True, n_iter=3, init=[0.0630, 0.2156], phi=[0.0704, 0.1455]
    n_clones=3 best[0,1,2]: sum_rho=0.2149, cost=0.00641, ICL=-56.99, converged=True, n_iter=2, init=[0.0630, 0.1202, 0.2156], phi=[0.0632, 0.0583, 0.0934]
    n_clones=4 best[0,1,2,3]: sum_rho=0.2149, cost=0.00622, ICL=-54.42, converged=True, n_iter=2, init=[0.0487, 0.0630, 0.1202, 0.2156], phi=[0.0479, 0.0149, 0.0586, 0.0935]
    SELECTED (best-ICL): n_clones=3, ICL=-56.99, purity=0.2149 (4 models evaluated)
  Wrote 4581 probes to custom_Sig_18_tumor_normal_probe_agg.tsv.gz
   13 segments, 13 events, 255 genes
  Wrote 13 segments (13 events) to custom_Sig_18_tumor_normal_segments.tsv
  Wrote 13 segments to custom_Sig_18_tumor_normal.seg
  Wrote 1 metrics rows to custom_Sig_18_tumor_normal_metrics.tsv
  Wrote 255 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=4, n_segs=14, dipLogR=-0.0920
    Greedy search: 4 model combinations
    n_clones=1 best[0]: sum_rho=0.0302, cost=0.00191, ICL=-84.07, converged=True, n_iter=2, init=[0.0344], phi=[0.0302]
    n_clones=2 best[0,1]: sum_rho=0.1336, cost=0.01726, ICL=-51.59, converged=True, n_iter=2, init=[0.0344, 0.1345], phi=[0.0303, 0.1033]
    n_clones=3 best[0,1,2]: sum_rho=0.1349, cost=0.01674, ICL=-49.31, converged=True, n_iter=3, init=[0.0344, 0.0964, 0.1345], phi=[0.0312, 0.0636, 0.0400]
    n_clones=4 best[0,1,2,3]: sum_rho=0.4212, cost=0.01523, ICL=-48.56, converged=True, n_iter=5, init=[0.0344, 0.0964, 0.1345, 0.4207], phi=[0.0301, 0.0645, 0.0387, 0.2879]
    SELECTED (best-ICL): n_clones=1, ICL=-84.07, purity=0.0302 (4 models evaluated)
   14 segments, 14 events
  Wrote 14 segments to ./tumor_only/custom_Sig_18_tumor_normal.seg
  Wrote 4581 probes to ./tumor_only/custom_Sig_18_tumor_normal_probe_agg.tsv.gz
    custom_Sig_18_tumor_normal (blood)...

Command error:
  /usr/local/lib/python3.12/site-packages/sklearn/base.py:1403: ConvergenceWarning: Number of distinct clusters (10) 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 (10) 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 (10) 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 (10) 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 (10) 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 (10) 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 (10) 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 (10) 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 (10) 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 (10) 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 (10) 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 (10) 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 (10) 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 (10) 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 (10) 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 (10) 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 (10) 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 1757, in run_germline_decomp
      fit_result = fit_diploid_logr(df, dipLogR_range=germ_dipLogR_range,
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/usr/local/bin/clonal_decomp.py", line 417, in fit_diploid_logr
      "fold_cost_curves": fold_cost_curves,
                          ^^^^^^^^^^^^^^^^
  UnboundLocalError: cannot access local variable 'fold_cost_curves' where it is not associated with a value

Work dir:
  s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/dd/87980384faeef2bfbac3966189a161

Container:
  292967571998.dkr.ecr.us-west-2.amazonaws.com/soma-cnv:20260604-9c39aac

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`