Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8d/529a19c2fbc83b02cf60d75fcade22/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-1b08ba89-f5a0-482c-af91-0dd20f879cef/38/2bb9d67738f419183fdf9d0538f39e/gene_tiers.yaml
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8d/529a19c2fbc83b02cf60d75fcade22/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/eb/cf44bf1786ed8552ed2fcee1041992/test_harmonized_calls.tsv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/00/d3fd7e7182e218164b19ce677d5d82/truth_harmonized_calls.tsv
==> STAGING COMPLETE (5 inputs)
Traceback (most recent call last):
File "/tmp/nxf.G0xrOqZAEq/nextflow-bin/resolve_gene_tier.py", line 102, in <module>
main()
File "/tmp/nxf.G0xrOqZAEq/nextflow-bin/resolve_gene_tier.py", line 88, in main
gene_set = gene_set_from_tier_spec(match, yaml_dir)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/tmp/nxf.G0xrOqZAEq/nextflow-bin/resolve_gene_tier.py", line 34, in gene_set_from_tier_spec
df = pd.read_csv(p, header=None)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 873, in read_csv
return _read(filepath_or_buffer, kwds)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 300, in _read
parser = TextFileReader(filepath_or_buffer, **kwds)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1645, in __init__
self._engine = self._make_engine(f, self.engine)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1904, in _make_engine
self.handles = get_handle(
^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/pandas/io/common.py", line 930, in get_handle
handle = open(
^^^^^
FileNotFoundError: [Errno 2] No such file or directory: '/tmp/nxf.G0xrOqZAEq/TSO500_RNAgenelist.txt'