Error executing process > 'SOMATIC_CNV_CALLING:SOMA_CNV_NORMALIZE (1029_01S-N1-BDNA-1_B23KGCJLT4_1)'

Caused by:
  Process `SOMATIC_CNV_CALLING:SOMA_CNV_NORMALIZE (1029_01S-N1-BDNA-1_B23KGCJLT4_1)` terminated with an error exit status (1)


Command executed:

  SEX=$(python3 -c "
  import pandas as pd
  sex = pd.read_csv('sex_calls.csv')
  lookup = dict(zip(sex['specimen_id'], sex['inferred_sex']))
  s = lookup.get('1029_01S', 'unknown')
  print('male' if s != 'female' else 'female')
  ")
  
  python /usr/local/bin/normalize_sample.py \
      --counts 1029_01S-N1-BDNA-1_B23KGCJLT4_1_probes.tsv.gz \
      --batch-reference batch_reference.parquet \
      --gc-reference /usr/local/share/probe_gc_content.tsv \
      --sex $SEX \
      --sample-id 1029_01S-N1-BDNA-1_B23KGCJLT4_1 \
      --specimen-id 1029_01S \
      --flowcell B23KFCWLT4 \
      --sample-type normal \
      --output 1029_01S-N1-BDNA-1_B23KGCJLT4_1_normalized.parquet \
      --feature-stats-output 1029_01S-N1-BDNA-1_B23KGCJLT4_1_gam_stats.json

Command exit status:
  1

Command output:
  (empty)

Command error:
  Loaded 472,386 probes for 1029_01S-N1-BDNA-1_B23KGCJLT4_1
    Sex homology mask: 1494 probes set to mask=2
    5-feature GAM: R²=0.9648
  Traceback (most recent call last):
    File "/usr/local/bin/normalize_sample.py", line 187, in <module>
      normalize_one_sample(
    File "/usr/local/bin/normalize_sample.py", line 121, in normalize_one_sample
      os.makedirs(os.path.dirname(output_path), exist_ok=True)
    File "<frozen os>", line 225, in makedirs
  FileNotFoundError: [Errno 2] No such file or directory: ''

Work dir:
  s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/64/49d75703251a47e5bd38358486694c

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

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