EmptyDataError: No columns to parse from file

[Mu Dong]

Hi all,

It is my first time using this platform. 

After submitting my file, it ran for 19min then failed the analysis, saying :EmptyDataError: No columns to parse from file.

The original file is raw thermofisher, I converted to MZML. don't know where went wrong.

below are the messages. Your help is really appreciated.

Thanks！

FAILED

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Traceback (most recent call last): File "/data/ccms-gnps/tools/molecularsearch/release_28/getGNPS_library_annotations.py", line 208, in <module> main() File "/data/ccms-gnps/tools/molecularsearch/release_28/getGNPS_library_annotations.py", line 205, in main enrich_output(input_result_filename, output_result_filename) File "/data/ccms-gnps/tools/molecularsearch/release_28/getGNPS_library_annotations.py", line 16, in enrich_output input_results_df = pd.read_csv(input_filename, sep="\t") File "/data/ccms-gnps/tools/miniconda3_gamma/lib/python3.7/site-packages/pandas/io/parsers.py", line 676, in parser_f return _read(filepath_or_buffer, kwds) File "/data/ccms-gnps/tools/miniconda3_gamma/lib/python3.7/site-packages/pandas/io/parsers.py", line 448, in _read parser = TextFileReader(fp_or_buf, **kwds) File "/data/ccms-gnps/tools/miniconda3_gamma/lib/python3.7/site-packages/pandas/io/parsers.py", line 880, in __init__ self._make_engine(self.engine) File "/data/ccms-gnps/tools/miniconda3_gamma/lib/python3.7/site-packages/pandas/io/parsers.py", line 1114, in _make_engine self._engine = CParserWrapper(self.f, **self.options) File "/data/ccms-gnps/tools/miniconda3_gamma/lib/python3.7/site-packages/pandas/io/parsers.py", line 1891, in __init__ self._reader = parsers.TextReader(src, **kwds) File "pandas/_libs/parsers.pyx", line 532, in pandas._libs.parsers.TextReader.__cinit__ pandas.errors.EmptyDataError: No columns to parse from file Tool execution terminates abnormally with exit code [1]

[Mingxun Wang]

The file you selected isnt mzML file. I'd recommend checking the conversion again. 

In case it helps, try out our quickstart:

https://gnps-quickstart.ucsd.edu/conversion

Best,

Ming

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[Mu Dong]

Thanks Ming,

I used the WINSCP to convert my thermofisher raw data to the mzML based on the step from the website. I see the file is in mzML format. Not sure why it is diagnosed the file isnt mzML? 

Or you mean the original file I used to convert to mzML was wrong? 

looking forwards to your reply.

[Mingxun Wang]

I think you might be using the wrong software to convert your data. If you get a chance, take a look at this documentation:

https://ccms-ucsd.github.io/GNPSDocumentation/fileconversion/

Ming

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[Mu Dong]

Thanks Ming,

Sorry I should mean MSconvert instead of WINSCP. 

I followed steps on the link you provided using the recommended converter.

Best regards,

Ning

[Mingxun Wang]

What you selected is not an mzML file:

burdekin/Y1.6