Error executing process > 'SOMATIC_CNV_CALLING:SOMA_CNV_NORMALIZE (1)'

Caused by:
  Can't stage file /ai-pipelines-experiment/chnobles/test_image_rename/results/norm_reference/batch_reference.parquet -- file does not exist


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_0W2', 'unknown')
  print('male' if s != 'female' else 'female')
  ")
  
  python /usr/local/bin/normalize_sample.py \
      --counts 1029_0W2-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_0W2-N1-BDNA-1_B23KGCJLT4_1 \
      --specimen-id 1029_0W2 \
      --flowcell A23KCGYLT4 \
      --sample-type normal \
      --output 1029_0W2-N1-BDNA-1_B23KGCJLT4_1_normalized.parquet \
      --feature-stats-output 1029_0W2-N1-BDNA-1_B23KGCJLT4_1_gam_stats.json

Command exit status:
  -

Command output:
  (empty)

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

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