MASST (SEARCH_SINGLE_SPECTRUM v28) ERROR

[Daniel Alvarado]

Hi everyone, I've been running single spectrum searches with MASST, and in some cases I keep getting this error:

 Traceback (most recent call last): File "/data/ccms-gnps/tools/search_single_spectrum/release_28/foodomics_track.py", line 64, in <module> main() File "/data/ccms-gnps/tools/search_single_spectrum/release_28/foodomics_track.py", line 56, in main matches_df = pd.read_csv(args.matches_results, sep="\t") File "/data/ccms-gnps/tools/anaconda3/lib/python3.5/site-packages/pandas/io/parsers.py", line 709, in parser_f return _read(filepath_or_buffer, kwds) File "/data/ccms-gnps/tools/anaconda3/lib/python3.5/site-packages/pandas/io/parsers.py", line 449, in _read parser = TextFileReader(filepath_or_buffer, **kwds) File "/data/ccms-gnps/tools/anaconda3/lib/python3.5/site-packages/pandas/io/parsers.py", line 818, in __init__ self._make_engine(self.engine) File "/data/ccms-gnps/tools/anaconda3/lib/python3.5/site-packages/pandas/io/parsers.py", line 1049, in _make_engine self._engine = CParserWrapper(self.f, **self.options) File "/data/ccms-gnps/tools/anaconda3/lib/python3.5/site-packages/pandas/io/parsers.py", line 1695, in __init__ self._reader = parsers.TextReader(src, **kwds) File "pandas/_libs/parsers.pyx", line 565, in pandas._libs.parsers.TextReader.__cinit__ pandas.errors.EmptyDataError: No columns to parse from file Tool execution terminates abnormally with exit code [1] 

Link to the task: https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=3823145d5c7f4a2cb9dbb9635c435581

I've checked thoroughly the input of the data to make sure I'm not introducing any errors, but that doesn't seem to be the problem.

Any advice on how to solve it would be greatly appreciated.

Thanks,

Daniel

[Daniel Alvarado]

P.S.: I ran the same data on v27 and it worked without errors

[Jenan Kharbush]

I'm getting the same error; interested to hear if there's a solution. I clicked on the "Masst spectrum" button from within some molecular networking results, and didn't change any of the default settings within the workflow.

[Mingxun Wang]

Thanks for letting us know. We've noticed a few bugs in release 28 and we're readying a fix for them. It seems to be when there are no match results it gives some errors, but we'll get it addressed!

Best,

Ming

[Daniel Alvarado]

Perfect, thank you very much for the reply.

Daniel

[Mingxun Wang]

Forgot to respond, but new release is live, if you want to clone to latest should hopefully fix these errors. 

Ming

[Daniel Alvarado]

Ran it on the latest version and it worked perfectly, thanks a lot!

Daniel