Describe the bug
Hi, when I run MOLECULAR-LIBRARYSEARCH-V2 (version release_28) with a colelction of mgf spectra I get an persistant error and have narrowed it down to one spectrum.
The input file for that spectrum looks like this:
BEGIN IONS
SCANS=1470
TITLE=file HILIC.n__HCD.nearest.neg; msLevel 2; retentionTime 85.99919; scanNum 252; scanIndex 252; precMz 292.9459; precCharge 1
RTINSECONDS=85.99919
PEPMASS=292.9459
CHARGE=1-
FEATURE_ID=1470
FEATURE_MASSTAG=HILIC.n__M292.9460T86
58.111743927002 14461.34375
96.9599990844727 241147.296875
102.795135498047 14190.599609375
130.439208984375 14969.1572265625
130.794021606445 14021.1611328125
214.914184570312 216550.75
220.146362304688 36298.15234375
221.154891967773 64049.296875
227.698944091797 52251.109375
227.728271484375 27764.72265625
232.924285888672 180840.703125
235.520782470703 16272.595703125
236.105178833008 31650.90234375
256.871948242188 24619.908203125
274.880920410156 5340550
274.958435058594 41318.74609375
275.880767822266 27676.9296875
292.891571044922 571594.5
293.178527832031 189726.84375
END IONS
The output failure is this:
['spectra/spec-00000.mgf']
['spectra/spec-00000.mgf']
Parallel to execute 1
/data/ccms-gnps/tools/molecularsearch/release_28/main_execmodule.allcandidates ExecSpectralLibrarySearchMolecular temp/24691b6c-652a-454c-9151-2d1fa08bec7d.params -ccms_input_spectradir temp -ccms_results_prefix tempresults -ll 9
Invalid number of rows for key None 2 23
Traceback (most recent call last):
File "/data/ccms-gnps/tools/molecularsearch/release_28/searchlibrarysearch_molecularv2_parallelstep.py", line 167, in
main()
File "/data/ccms-gnps/tools/molecularsearch/release_28/searchlibrarysearch_molecularv2_parallelstep.py", line 156, in main
ming_fileio_library.write_list_dict_table_data(full_result_list, os.path.join(args.result_folder, str(uuid.uuid4()) + ".tsv"))
File "/data/ccms-gnps/tools/molecularsearch/release_28/ming_fileio_library.py", line 162, in write_list_dict_table_data
write_dictionary_table_data(output_dict, output_filename, header_list=header_list)
File "/data/ccms-gnps/tools/molecularsearch/release_28/ming_fileio_library.py", line 129, in write_dictionary_table_data
header_list.sort()
TypeError: unorderable types: NoneType() < str()
Tool execution terminates abnormally with exit code [1]
This is run with the followign parameters:
Precursor Ion Mass Tolerance: 2
Min Matched Peaks: 3
Fragment Ion Mass Tolerance: 0.5
Score Threshold: |0.5
Libray Class: Bronze
Top Hits Per Spectrum: 3
Filter peaks in 50Da Window: Don't Filter
The job ID is:
ID=a6d4a47808914aedb95184c4873c3d4e
Describe the bug
Hi, when I run MOLECULAR-LIBRARYSEARCH-V2 (version release_28) with a colelction of mgf spectra I get an persistant error and have narrowed it down to one spectrum.
The input file for that spectrum looks like this:
BEGIN IONS
SCANS=1470
TITLE=file HILIC.n__HCD.nearest.neg; msLevel 2; retentionTime 85.99919; scanNum 252; scanIndex 252; precMz 292.9459; precCharge 1
RTINSECONDS=85.99919
PEPMASS=292.9459
CHARGE=1-
FEATURE_ID=1470
FEATURE_MASSTAG=HILIC.n__M292.9460T86
58.111743927002 14461.34375
96.9599990844727 241147.296875
102.795135498047 14190.599609375
130.439208984375 14969.1572265625
130.794021606445 14021.1611328125
214.914184570312 216550.75
220.146362304688 36298.15234375
221.154891967773 64049.296875
227.698944091797 52251.109375
227.728271484375 27764.72265625
232.924285888672 180840.703125
235.520782470703 16272.595703125
236.105178833008 31650.90234375
256.871948242188 24619.908203125
274.880920410156 5340550
274.958435058594 41318.74609375
275.880767822266 27676.9296875
292.891571044922 571594.5
293.178527832031 189726.84375
END IONS
The output failure is this:
['spectra/spec-00000.mgf']
['spectra/spec-00000.mgf']
Parallel to execute 1
/data/ccms-gnps/tools/molecularsearch/release_28/main_execmodule.allcandidates ExecSpectralLibrarySearchMolecular temp/24691b6c-652a-454c-9151-2d1fa08bec7d.params -ccms_input_spectradir temp -ccms_results_prefix tempresults -ll 9
Invalid number of rows for key None 2 23
Traceback (most recent call last):
File "/data/ccms-gnps/tools/molecularsearch/release_28/searchlibrarysearch_molecularv2_parallelstep.py", line 167, in
main()
File "/data/ccms-gnps/tools/molecularsearch/release_28/searchlibrarysearch_molecularv2_parallelstep.py", line 156, in main
ming_fileio_library.write_list_dict_table_data(full_result_list, os.path.join(args.result_folder, str(uuid.uuid4()) + ".tsv"))
File "/data/ccms-gnps/tools/molecularsearch/release_28/ming_fileio_library.py", line 162, in write_list_dict_table_data
write_dictionary_table_data(output_dict, output_filename, header_list=header_list)
File "/data/ccms-gnps/tools/molecularsearch/release_28/ming_fileio_library.py", line 129, in write_dictionary_table_data
header_list.sort()
TypeError: unorderable types: NoneType() < str()
Tool execution terminates abnormally with exit code [1]
This is run with the followign parameters:
Precursor Ion Mass Tolerance: 2
Min Matched Peaks: 3
Fragment Ion Mass Tolerance: 0.5
Score Threshold: |0.5
Libray Class: Bronze
Top Hits Per Spectrum: 3
Filter peaks in 50Da Window: Don't Filter
The job ID is:
ID=a6d4a47808914aedb95184c4873c3d4e