Error executing process > 'NFCORE_SAREK:SAREK:AIH_CNV:ProcessBatch (aih_cnv_cohort_aih_cnv_process_batch)'

Caused by:
  Process `NFCORE_SAREK:SAREK:AIH_CNV:ProcessBatch (aih_cnv_cohort_aih_cnv_process_batch)` terminated with an error exit status (1)


Command executed:

  # Reconstruct samples/<sample_id>/counts.tsv directory structure expected by the tool.
  # Each file is named <sample_id>__counts.tsv — parse the sample_id from the filename.
  for f in *__counts.tsv; do
      sid="${f%__counts.tsv}"
      mkdir -p samples/${sid}/
      cp ${f} samples/${sid}/counts.tsv
  done
  cnv_pipe process-batch \
           input.csv \
           altera_v3_panel.bed \
           altera_v3_variable_regions.bed \
           $(pwd) \
           counts.parquet \
           sample_metrics.parquet \
           ploidy.parquet \
           aih_cnv_cohort__sex_calls.parquet \
           aih_cnv_cohort__sex_calls.png \
           --max-workers 16

Command exit status:
  1

Command output:
  (empty)

Command error:
  2026-02-27 23:50:38,808 - cnv_pipe.cnv_pipe.batch.ess - WARNING - Not enough samples (2) compared to nearby probes (2) for probe 15608. MinCovDet requires more samples than features.
  2026-02-27 23:50:38,808 - cnv_pipe.cnv_pipe.batch.ess - WARNING - Not enough samples (2) compared to nearby probes (2) for probe 15609. MinCovDet requires more samples than features.
  /usr/local/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:793: UserWarning: The covariance matrix associated to your dataset is not full rank
  /usr/local/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:793: UserWarning: The covariance matrix associated to your dataset is not full rank
  Traceback (most recent call last):
    File "/usr/local/lib/python3.12/site-packages/metaflow/multicore_utils.py", line 65, in _spawn
      ret = func(arg)
            ^^^^^^^^^
    File "/usr/local/lib/python3.12/site-packages/metaflow/multicore_utils.py", line 170, in wrapper
      return idx, func(arg)
                  ^^^^^^^^^
    File "/usr/local/lib/python3.12/site-packages/cnv_pipe/batch/ess.py", line 103, in get_chunk_weights
      counts_iter = imputer.fit_transform(counts_iter)
                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/usr/local/lib/python3.12/site-packages/sklearn/utils/_set_output.py", line 316, in wrapped
      data_to_wrap = f(self, X, *args, **kwargs)
                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/usr/local/lib/python3.12/site-packages/sklearn/base.py", line 907, in fit_transform
      return self.fit(X, **fit_params).transform(X)
             ^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/usr/local/lib/python3.12/site-packages/sklearn/base.py", line 1336, in wrapper
      return fit_method(estimator, *args, **kwargs)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/usr/local/lib/python3.12/site-packages/sklearn/impute/_base.py", line 447, in fit
      X = self._validate_input(X, in_fit=True)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/usr/local/lib/python3.12/site-packages/sklearn/impute/_base.py", line 374, in _validate_input
      raise ve
    File "/usr/local/lib/python3.12/site-packages/sklearn/impute/_base.py", line 355, in _validate_input
      X = validate_data(
          ^^^^^^^^^^^^^^
    File "/usr/local/lib/python3.12/site-packages/sklearn/utils/validation.py", line 2902, in validate_data
      out = check_array(X, input_name="X", **check_params)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/usr/local/lib/python3.12/site-packages/sklearn/utils/validation.py", line 1106, in check_array
      raise ValueError(
  ValueError: Found array with 0 feature(s) (shape=(3, 0)) while a minimum of 1 is required by SimpleImputer.
  /usr/local/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:793: UserWarning: The covariance matrix associated to your dataset is not full rank
  /usr/local/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:793: UserWarning: The covariance matrix associated to your dataset is not full rank
  /usr/local/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:793: UserWarning: The covariance matrix associated to your dataset is not full rank
  /usr/local/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:793: UserWarning: The covariance matrix associated to your dataset is not full rank
  /usr/local/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:793: UserWarning: The covariance matrix associated to your dataset is not full rank
  /usr/local/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:793: UserWarning: The covariance matrix associated to your dataset is not full rank
  /usr/local/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:793: UserWarning: The covariance matrix associated to your dataset is not full rank
  /usr/local/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:793: UserWarning: The covariance matrix associated to your dataset is not full rank
  /usr/local/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:793: UserWarning: The covariance matrix associated to your dataset is not full rank
  /usr/local/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-9.251797923545029 > -43.890560105369012). You may want to try with a higher value of support_fraction (current value: 0.600).
  /usr/local/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-9.251797923545029 > -43.890560105369012). You may want to try with a higher value of support_fraction (current value: 0.600).
  /usr/local/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-9.251797923545029 > -43.890560105369012). You may want to try with a higher value of support_fraction (current value: 0.600).
  /usr/local/lib/python3.12/site-packages/sklearn/covariance/_robust_covariance.py:188: RuntimeWarning: Determinant has increased; this should not happen: log(det) > log(previous_det) (-9.251797923545029 > -43.890560105369012). You may want to try with a higher value of support_fraction (current value: 0.600).

Work dir:
  s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a5/02e3d86a17acada3bd4cd1cfc9d115

Container:
  292967571998.dkr.ecr.us-west-2.amazonaws.com/cgp-horizon_cnv_pipe:patched-max-workers-8

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`