GC-MS Analysis Library matching - FBMN

[montmasis]

Hi,
I am still having problems with the GC-MS Analysis Library matching (FBMN) with data originally pre-processed in MS-DIAL.

The job works fine when I am not using the retention index library function. When I use the retention index, I get the error (below).

The "carbon marker" (csv) file I got as a template example from Alexander Aksenov looks like mine, beside that I have more alkanes (and I do not have C8):
Alexander --> C8-C26
Me --> C9-C40

Alexander thinks it could be a parsing issue and/or a missing library..

This the job that fails (below the error)
https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=a7b11d597711495284a2c3c172bef2a3

Thanks in advance

Stefano

---

Carbon_Marker_File/Carbon_Marker_File-00000.csv
Traceback (most recent call last):
File "/data/ccms-gnps/tools/molecularsearch-gc/release_23/calculate_kovats.py", line 69, in
main()
File "/data/ccms-gnps/tools/molecularsearch-gc/release_23/calculate_kovats.py", line 66, in main
args.output_library_identifications)
File "/data/ccms-gnps/tools/molecularsearch-gc/release_23/calculate_kovats.py", line 39, in calculate_kovats
identifications_df = pd.read_csv(input_identifications_filename, 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]

[mwang87]

Seems your data has no identifications to the libraries. We'll have to handle that. Thanks for letting us know!

[montmasis]

Yes the identification was because I used the high-res settings suggested for Orbitrap as in the tutorial. But Alexander said they were too narrow, so I used 0.4 Da instead and I got 100+ hits. The main problem now is the retention index, carbon marker. I always get an error with that and I don't know why

…

On Thu, Jul 2, 2020, 06:26 Ming Wang ***@***.***> wrote: Seems your data has no identifications to the libraries. We'll have to handle that. Thanks for letting us know! — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#567 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADRG2CWUGHPADLPAFG7HOC3RZQD7TANCNFSM4OMDMINA> .

[montmasis]

when I do get hits with the new settings, the carbon marker doesn´t give an error anymore. However, I do not get any Kovats Indexes calculated in the hits table: https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=7458f345754745be875011863b802d0b I tried with RT reported both in minutes and seconds in the carbon marker table On Thu, Jul 2, 2020 at 10:46 AM stefano papazian <montmasis@gmail.com> wrote:

…

Yes the identification was because I used the high-res settings suggested for Orbitrap as in the tutorial. But Alexander said they were too narrow, so I used 0.4 Da instead and I got 100+ hits. The main problem now is the retention index, carbon marker. I always get an error with that and I don't know why On Thu, Jul 2, 2020, 06:26 Ming Wang ***@***.***> wrote: > Seems your data has no identifications to the libraries. We'll have to > handle that. Thanks for letting us know! > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub > <#567 (comment)>, > or unsubscribe > <https://github.com/notifications/unsubscribe-auth/ADRG2CWUGHPADLPAFG7HOC3RZQD7TANCNFSM4OMDMINA> > . >