Error running ms2query

[ShinyBasu]

Hello,

I have been trying to process .mgf files generated with MZMine with ms2query. I got the following error (detailed screenshot attached below): RuntimeError: PytorchStreamReader failed reading zip archive: failed finding central directory

I have precious little experience with Python and any tips on fixing this would be greatly appreciated.

[niekdejonge]

Hi @ShinyBasu, I don't directly recognize the error. But it sounds like the model you are loading in might be of an incorrect format. Did you download the models by running: ms2query --library .\folder_to_store_the_library --download --ionmode positive

You can replace the .\folder_to_store_the_library with the location where you want to store the library.

after that you can run: ms2query --spectra .\Blanks_MZMine --library .\folder_to_store_the_library --ionmode positive

[ShinyBasu]

Sir,

Thank you for your reply. I have downloaded the entire library as per the instructions (screenshot attached). However, the command you suggested returned the following error (attached below). I would be very grateful if you could suggest a fix.

Thanking you

On Fri, Sep 27, 2024 at 2:57 PM Niek de Jonge @.***> wrote:

Hi @ShinyBasu https://github.com/ShinyBasu, I don't directly recognize the error. But it sounds like the model you are loading in might be of an incorrect format. Did you download the models by running: ms2query --library .\folder_to_store_the_library --download --ionmode positive

You can replace the .\folder_to_store_the_library with the location where you want to store the library.

after that you can run: ms2query --spectra .\Blanks_MZMine --library .\folder_to_store_the_library --ionmode positive

— Reply to this email directly, view it on GitHub https://github.com/iomega/ms2query/issues/254#issuecomment-2378849557, or unsubscribe https://github.com/notifications/unsubscribe-auth/AZG6GV7HT67GT4VEY6NYPV3ZYUQINAVCNFSM6AAAAABO6UOZO6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNZYHA2DSNJVG4 . You are receiving this because you were mentioned.Message ID: @.***>

-- Shayontani Basu UGC- NTA NET SRF School of Environmental Studies Jadavpur University

[ShinyBasu]

Sir, I am writing to update you that I have successfully run ms2query on my data. The problem was that the ms2deepscore model is not downloading completely via the command line. I manually downloaded all the files and stored them in a new folder within the "folder_to_store_the_library". I then ran the command: ms2query --spectra .\Blanks_MZMine --library .\new_folder --ionmode positive

This worked.

Thanking you

On Fri, Sep 27, 2024 at 8:37 PM Shayontani Basu @.***> wrote:

Sir,

Thank you for your reply. I have downloaded the entire library as per the instructions (screenshot attached). However, the command you suggested returned the following error (attached below). I would be very grateful if you could suggest a fix.

Thanking you

On Fri, Sep 27, 2024 at 2:57 PM Niek de Jonge @.***> wrote:

Hi @ShinyBasu https://github.com/ShinyBasu, I don't directly recognize the error. But it sounds like the model you are loading in might be of an incorrect format. Did you download the models by running: ms2query --library .\folder_to_store_the_library --download --ionmode positive

You can replace the .\folder_to_store_the_library with the location where you want to store the library.

after that you can run: ms2query --spectra .\Blanks_MZMine --library .\folder_to_store_the_library --ionmode positive

— Reply to this email directly, view it on GitHub https://github.com/iomega/ms2query/issues/254#issuecomment-2378849557, or unsubscribe https://github.com/notifications/unsubscribe-auth/AZG6GV7HT67GT4VEY6NYPV3ZYUQINAVCNFSM6AAAAABO6UOZO6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNZYHA2DSNJVG4 . You are receiving this because you were mentioned.Message ID: @.***>

-- Shayontani Basu UGC- NTA NET SRF School of Environmental Studies Jadavpur University

-- Shayontani Basu UGC- NTA NET SRF School of Environmental Studies Jadavpur University