Error executing process > 'RECALL:AGGREGATE_TRUTH_CALLS (truth)'

Caused by:
  Process `RECALL:AGGREGATE_TRUTH_CALLS (truth)` terminated with an error exit status (1)


Command executed:

  aggregate_harmonized_calls.py \
      --discovered truth_matches.tsv \
      --fusion-column truth_fusion_tsv \
      --manifest sample_manifest.tsv \
      --output truth_harmonized_calls.tsv
  
  cat <<-END_VERSIONS > versions.yml
  "RECALL:AGGREGATE_TRUTH_CALLS":
      python: $(python --version 2>&1 | sed 's/Python //')
      aggregate_harmonized_calls: "1.0.0"
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
    File "/usr/local/lib/python3.11/site-packages/fsspec/core.py", line 147, in open
      return self.__enter__()
             ^^^^^^^^^^^^^^^^
    File "/usr/local/lib/python3.11/site-packages/fsspec/core.py", line 105, in __enter__
      f = self.fs.open(self.path, mode=mode)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/usr/local/lib/python3.11/site-packages/fsspec/spec.py", line 1352, in open
      f = self._open(
          ^^^^^^^^^^^
    File "/usr/local/lib/python3.11/site-packages/s3fs/core.py", line 816, in _open
      return S3File(
             ^^^^^^^
    File "/usr/local/lib/python3.11/site-packages/s3fs/core.py", line 2556, in __init__
      super().__init__(
    File "/usr/local/lib/python3.11/site-packages/fsspec/spec.py", line 1926, in __init__
      self.size = self.details["size"]
                  ^^^^^^^^^^^^
    File "/usr/local/lib/python3.11/site-packages/fsspec/spec.py", line 1939, in details
      self._details = self.fs.info(self.path)
                      ^^^^^^^^^^^^^^^^^^^^^^^
    File "/usr/local/lib/python3.11/site-packages/fsspec/asyn.py", line 118, in wrapper
      return sync(self.loop, func, *args, **kwargs)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/usr/local/lib/python3.11/site-packages/fsspec/asyn.py", line 103, in sync
      raise return_result
    File "/usr/local/lib/python3.11/site-packages/fsspec/asyn.py", line 56, in _runner
      result[0] = await coro
                  ^^^^^^^^^^
    File "/usr/local/lib/python3.11/site-packages/s3fs/core.py", line 1791, in _info
      raise FileNotFoundError(path)
  FileNotFoundError: natera-platform-sandbox/pipeline-outputs/aih_dev/altera_exact/hmnz__cgp_rna_exp0034__2fc40342--20260601/659_bdp_T1_TRNA_1_B2372Y3LT4_1/variants/rna_fusion/659_bdp_T1_TRNA_1_B2372Y3LT4_1.rnafusions.sendout_hg38.hmnz.tsv
  
  During handling of the above exception, another exception occurred:
  
  Traceback (most recent call last):
    File "/tmp/nxf.2yC3BPOLqQ/nextflow-bin/aggregate_harmonized_calls.py", line 66, in <module>
      main()
    File "/tmp/nxf.2yC3BPOLqQ/nextflow-bin/aggregate_harmonized_calls.py", line 45, in main
      df = read_csv(fusion_path, sep="\t", dtype=str)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/tmp/nxf.2yC3BPOLqQ/nextflow-bin/io_utils.py", line 87, in read_csv
      subprocess.run(["aws", "s3", "cp", path, tmp.name], check=True)
    File "/usr/local/lib/python3.11/subprocess.py", line 548, in run
      with Popen(*popenargs, **kwargs) as process:
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/usr/local/lib/python3.11/subprocess.py", line 1026, in __init__
      self._execute_child(args, executable, preexec_fn, close_fds,
    File "/usr/local/lib/python3.11/subprocess.py", line 1955, in _execute_child
      raise child_exception_type(errno_num, err_msg, err_filename)
  FileNotFoundError: [Errno 2] No such file or directory: 'aws'

Work dir:
  s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/09/7f915c8dd7212c259aa5d00a4389ef

Container:
  292967571998.dkr.ecr.us-west-2.amazonaws.com/rnafusion-performance-s3-python:1.0.0

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