Error with SWATH data

[Jo Ka]

Hello guys,

i got some strange errors while using for the first time SWATH data instead of DDA. I converted also to mzML but then this error apears minutes after submitting. Does someone know about these trouble with SWATH data or what might be another reason for this error. Every advise is welcome.

Error message:

Traceback (most recent call last): File "pandas/_libs/parsers.pyx", line 1130, in pandas._libs.parsers.TextReader._convert_tokens File "pandas/_libs/parsers.pyx", line 1254, in pandas._libs.parsers.TextReader._convert_with_dtype File "pandas/_libs/parsers.pyx", line 1269, in pandas._libs.parsers.TextReader._string_convert File "pandas/_libs/parsers.pyx", line 1459, in pandas._libs.parsers._string_box_utf8 UnicodeDecodeError: 'utf-8' codec can't decode byte 0xe4 in position 24: invalid continuation byte During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/data/ccms-gnps/tools/metabolomicsnetsv2/release_30/scripts/format_metadata.py", line 91, in <module> main() File "/data/ccms-gnps/tools/metabolomicsnetsv2/release_30/scripts/format_metadata.py", line 19, in main process(args.param_xml, args.metadata_folder, args.output_metadata_folder) File "/data/ccms-gnps/tools/metabolomicsnetsv2/release_30/scripts/format_metadata.py", line 29, in process user_metadata_df = pd.read_csv(input_metadata_filenames[0], 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 454, in _read data = parser.read(nrows) File "/data/ccms-gnps/tools/miniconda3_gamma/lib/python3.7/site-packages/pandas/io/parsers.py", line 1133, in read ret = self._engine.read(nrows) File "/data/ccms-gnps/tools/miniconda3_gamma/lib/python3.7/site-packages/pandas/io/parsers.py", line 2037, in read data = self._reader.read(nrows) File "pandas/_libs/parsers.pyx", line 860, in pandas._libs.parsers.TextReader.read File "pandas/_libs/parsers.pyx", line 875, in pandas._libs.parsers.TextReader._read_low_memory File "pandas/_libs/parsers.pyx", line 952, in pandas._libs.parsers.TextReader._read_rows File "pandas/_libs/parsers.pyx", line 1084, in pandas._libs.parsers.TextReader._convert_column_data File "pandas/_libs/parsers.pyx", line 1137, in pandas._libs.parsers.TextReader._convert_tokens File "pandas/_libs/parsers.pyx", line 1254, in pandas._libs.parsers.TextReader._convert_with_dtype File "pandas/_libs/parsers.pyx", line 1269, in pandas._libs.parsers.TextReader._string_convert File "pandas/_libs/parsers.pyx", line 1459, in pandas._libs.parsers._string_box_utf8 UnicodeDecodeError: 'utf-8' codec can't decode byte 0xe4 in position 24: invalid continuation byte Tool execution terminates abnormally with exit code [1]

Best

Jonas

[Mingxun Wang]

Hi Jonas,

Thanks for your question. Broadly DIA natively is not handled by Classical Networking, only DDA. I would recommend a tool like DIA Umpire which creates pseudo MS/MS so it mimics DDA data. 

Best,

Ming

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[Jo Ka]

Hi Ming,

thanks for your answer! I will give it a try! Meanwhile I remeasure the data set in DDA and try again with this new data set.

Best

Jonas

[Jo Ka]

Hi Ming,

I tried now with the new remeasured DDA data, but I get the exact same errors... so its not about the SWATH as I thought first. Do you might have any clue about the errors from my first message?

Status after 1 minute 10s:

FAILED

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---

Traceback (most recent call last): File "pandas/_libs/parsers.pyx", line 1130, in pandas._libs.parsers.TextReader._convert_tokens File "pandas/_libs/parsers.pyx", line 1254, in pandas._libs.parsers.TextReader._convert_with_dtype File "pandas/_libs/parsers.pyx", line 1269, in pandas._libs.parsers.TextReader._string_convert File "pandas/_libs/parsers.pyx", line 1459, in pandas._libs.parsers._string_box_utf8 UnicodeDecodeError: 'utf-8' codec can't decode byte 0xe4 in position 24: invalid continuation byte During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/data/ccms-gnps/tools/metabolomicsnetsv2/release_30/scripts/format_metadata.py", line 91, in <module> main() File "/data/ccms-gnps/tools/metabolomicsnetsv2/release_30/scripts/format_metadata.py", line 19, in main process(args.param_xml, args.metadata_folder, args.output_metadata_folder) File "/data/ccms-gnps/tools/metabolomicsnetsv2/release_30/scripts/format_metadata.py", line 29, in process user_metadata_df = pd.read_csv(input_metadata_filenames[0], 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 454, in _read data = parser.read(nrows) File "/data/ccms-gnps/tools/miniconda3_gamma/lib/python3.7/site-packages/pandas/io/parsers.py", line 1133, in read ret = self._engine.read(nrows) File "/data/ccms-gnps/tools/miniconda3_gamma/lib/python3.7/site-packages/pandas/io/parsers.py", line 2037, in read data = self._reader.read(nrows) File "pandas/_libs/parsers.pyx", line 860, in pandas._libs.parsers.TextReader.read File "pandas/_libs/parsers.pyx", line 875, in pandas._libs.parsers.TextReader._read_low_memory File "pandas/_libs/parsers.pyx", line 952, in pandas._libs.parsers.TextReader._read_rows File "pandas/_libs/parsers.pyx", line 1084, in pandas._libs.parsers.TextReader._convert_column_data File "pandas/_libs/parsers.pyx", line 1137, in pandas._libs.parsers.TextReader._convert_tokens File "pandas/_libs/parsers.pyx", line 1254, in pandas._libs.parsers.TextReader._convert_with_dtype File "pandas/_libs/parsers.pyx", line 1269, in pandas._libs.parsers.TextReader._string_convert File "pandas/_libs/parsers.pyx", line 1459, in pandas._libs.parsers._string_box_utf8 UnicodeDecodeError: 'utf-8' codec can't decode byte 0xe4 in position 24: invalid continuation byte Tool execution terminates abnormally with exit code [1]

Best

Jonas

Mingxun Wang schrieb am Donnerstag, 20. Juli 2023 um 01:03:47 UTC+2:

[Jo Ka]

Hi Ming,

the problem is solved! When I pasted some Informations in the metadata spreadsheet, it seems to give an error. I rewrote my metadata doc by hand and now it works fine.

Best

Jonas

[Mingxun Wang]

Hi Jonas!

Glad to hear it. 

Best,

Ming

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