Re: [GNPS Forum] Error in FBMN with Mzmine

[Osama Gomaa Mohamed]

Hi Nesrine,

I guess the problem is in the file format of MS2 data. MZmine2 output is mgf file while you are using txt file.

Best regards,

Osama

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Dr Osama Mohamed

BSc Pharm (Hons), MSc, PhD

Lecturer of Pharmacognosy

Pharmacognosy Department, Faculty of Pharmacy, Cairo University

Kasr El-Aini street, Cairo 11562, Egypt

M +201030797870

E osama....@pharma.cu.edu.eg

On Mon, Feb 15, 2021 at 1:10 AM 'nesrine hegazi' via GNPS Discussion Forum and Bug Reports <molecular_networ...@googlegroups.com> wrote:

Hi,

I am trying to run a FBMN with data processed with Mzmine, But I get this error message:

traceback (most recent call last): File "/data/ccms-gnps/tools/feature-based-molecular-networking/release_27/scripts/filter_spectra.py", line 18, in <module> spectrum_collection.load_from_mgf() File "/data/ccms-gnps/tools/feature-based-molecular-networking/release_27/scripts/ming_spectrum_library.py", line 48, in load_from_mgf self.spectrum_list = load_mgf_file(self.filename) File "/data/ccms-gnps/tools/feature-based-molecular-networking/release_27/scripts/ming_spectrum_library.py", line 618, in load_mgf_file peaks.append([float(peak_split[0]), float(peak_split[1])]) ValueError: could not convert string to float: 'filename' Tool execution terminates abnormally with exit code [1]

Can you please help me resolve this problem

The link to my job is:

https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=51efd6bdff3b4f75bd27e3651ebe69ea

Thanks in advance

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[nesrine hegazi]

Thanks Dr Osama

Seems that I uploaded the wrong file

Will try again