Cannot launch example

[MHJena]

Hey,

i am trying to use MAGMa-plus. I have downloaded everything accordingly and am trying to compute the example given.

Everything works fine until i enter this command from the example:

python MAGMa_plus.py annotate -c 0 -d 0 -b 3 -w 1 -s hmdb output.db

See stacktrace below. I have created an HMDB database by using the python script beforehand and set the correct path to that h,db database in the .ini file.

Any help would be appreciated.

python MAGMa_plus.py annotate -c 0 -d 0 -b 3 -w 1 -s hmdb output.db Parameter settings A Traceback (most recent call last): File "MAGMa_plus.py", line 435, in <module> main() File "MAGMa_plus.py", line 413, in main magmacommand.run(magma_arguments_l) File "/home/carsten/MAGMa-plus-master/MAGMa_script.py", line 249, in run return args.func(args) File "/home/carsten/MAGMa-plus-master/MAGMa_script.py", line 189, in annotate annotate_engine = magma_session.get_annotate_engine(skip_fragmentation=args.skip_fragmentation, max_broken_bonds=args.max_broken_bonds, max_water_losses=args.max_water_losses, ms_intensity_cutoff=args.ms_intensity_cutoff, msms_intensity_cutoff=args.msms_intensity_cutoff, use_all_peaks=args.use_all_peaks, adducts=args.adducts, force_adduct=args.force_adduct, max_charge=args.max_charge, call_back_url=args.call_back_url) File "/home/carsten/MAGMa-plus-master/magma/init.py", line 75, in get_annotate_engine return AnnotateEngine(self.db_session, skip_fragmentation, max_broken_bonds, max_water_losses, ms_intensity_cutoff, msms_intensity_cutoff, use_all_peaks, adducts, force_adduct, max_charge, call_back_url) File "/home/carsten/MAGMa-plus-master/magma/init.py", line 761, in init print ('SETTINGS FOR MATCHING PRECURSOR IONS AND CANDIDATES:') TypeError: unicode argument expected, got 'str'

[savantas]

Hello, Your question reached me well. I am in a busy period currently, but I will try to look into this as soon as possible. Dries

…

On Thu, Oct 8, 2020 at 9:25 PM MHJena ***@***.***> wrote: Hey, i am trying to use MAGMa-plus. I have downloaded everything accordingly and am trying to compute the example given. Everything works fine until i enter this command from the example: python MAGMa_plus.py annotate -c 0 -d 0 -b 3 -w 1 -s hmdb output.db See stacktrace below. I have created an HMDB database by using the python script beforehand and set the correct path to that h,db database in the .ini file. Any help would be appreciated. python MAGMa_plus.py annotate -c 0 -d 0 -b 3 -w 1 -s hmdb output.db Parameter settings A Traceback (most recent call last): File "MAGMa_plus.py", line 435, in <module> main() File "MAGMa_plus.py", line 413, in main magmacommand.run(magma_arguments_l) File "/home/carsten/MAGMa-plus-master/MAGMa_script.py", line 249, in run return args.func(args) File "/home/carsten/MAGMa-plus-master/MAGMa_script.py", line 189, in annotate annotate_engine = magma_session.get_annotate_engine(skip_fragmentation=args.skip_fragmentation, max_broken_bonds=args.max_broken_bonds, max_water_losses=args.max_water_losses, ms_intensity_cutoff=args.ms_intensity_cutoff, msms_intensity_cutoff=args.msms_intensity_cutoff, use_all_peaks=args.use_all_peaks, adducts=args.adducts, force_adduct=args.force_adduct, max_charge=args.max_charge, call_back_url=args.call_back_url) File "/home/carsten/MAGMa-plus-master/magma/init.py", line 75, in get_annotate_engine return AnnotateEngine(self.db_session, skip_fragmentation, max_broken_bonds, max_water_losses, ms_intensity_cutoff, msms_intensity_cutoff, use_all_peaks, adducts, force_adduct, max_charge, call_back_url) File "/home/carsten/MAGMa-plus-master/magma/init.py", line 761, in init print ('SETTINGS FOR MATCHING PRECURSOR IONS AND CANDIDATES:') TypeError: unicode argument expected, got 'str' — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#1>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADZ7ABP7SIBT27HLZE3M4CDSJYG2ZANCNFSM4SJFE3QQ> .