tycheyoung/homs-tc

homs-tc's Issues

.interim file not created

Hi! I just tried to push a couple of .mgf files through the workflow and I get the following error:

test.pkl does not exist. Running query preprocessing first...
[Query] Classify query by its charge
[Query] Vectorizing: Raw spectra to spectrum vector
[Query] Convert charge: 1 to npz
[Query] Convert charge: 4 to npz
[Query] Convert charge: 2 to npz
[Query] Convert charge: 3 to npz
[Query] Convert charge: 5 to npz
[Query] Convert charge: 6 to npz
[Query] Save query_spectra to pkl
charge,ref_encode_time,query_encode_time,search time,total time
Traceback (most recent call last):
  File "run.py", line 127, in <module>
    main()
  File "run.py", line 117, in main
    output_fname = fdr_postprocessing(std_interim_fname, open_interim_fname,
  File "/home/dnanexus/homs-tc/homs_tc/fdr_postprocessing.py", line 79, in fdr_postprocessing
    df_std = cuda_output_to_df(cuda_std_output)
  File "/home/dnanexus/homs-tc/homs_tc/fdr_postprocessing.py", line 14, in cuda_output_to_df
    df = pd.read_csv(cuda_output_fname, names=header_list, dtype=df_dtypes, delimiter="\t", header=None)
  File "/home/dnanexus/.local/lib/python3.8/site-packages/pandas/util/_decorators.py", line 211, in wrapper
    return func(*args, **kwargs)
  File "/home/dnanexus/.local/lib/python3.8/site-packages/pandas/util/_decorators.py", line 331, in wrapper
    return func(*args, **kwargs)
  File "/home/dnanexus/.local/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 950, in read_csv
    return _read(filepath_or_buffer, kwds)
  File "/home/dnanexus/.local/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 605, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
  File "/home/dnanexus/.local/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 1442, in __init__
    self._engine = self._make_engine(f, self.engine)
  File "/home/dnanexus/.local/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 1735, in _make_engine
    self.handles = get_handle(
  File "/home/dnanexus/.local/lib/python3.8/site-packages/pandas/io/common.py", line 856, in get_handle
    handle = open(
FileNotFoundError: [Errno 2] No such file or directory: 'test_std.interim'

Any help would be appreciated.