search

CCMS-UCSD / GNPS_Workflows

Public Workflows at GNPS
https://gnps.ucsd.edu/
Other
54 stars 44 forks source link

GNPS FBMN issue #872

Open lzlmby opened 8 months ago

lzlmby commented 8 months ago

I have been running MSDIAL based FBMN analysis. My data is from Thermo Orbitrap. I always get this error:

Columns (0,1,2,6,7,8,9,10,11,12,13,14,15,16,17,18,22,23,24) have mixed types. Specify dtype option on import or set low_memory=False. MSDIAL Traceback (most recent call last): File "/data/ccms-gnps/tools/feature-based-molecular-networking/release_28.2/scripts/reformat_quantification.py", line 135, in main() File "/data/ccms-gnps/tools/feature-based-molecular-networking/release_28.2/scripts/reformat_quantification.py", line 75, in main msdial_formatter.convert_to_feature_csv(args.quantification_table, args.quantification_table_reformatted) File "/data/ccms-gnps/tools/feature-based-molecular-networking/release_28.2/scripts/msdial_formatter.py", line 27, in convert_to_feature_csv scan = record["Alignment ID"] KeyError: 'Alignment ID' Tool execution terminates abnormally with exit code [1]

lfnothias commented 8 months ago

Hi, I believe this is related to the MSDIAL ver 5. Please check out this for a work around (either using ver 4 or the notebook) https://groups.google.com/u/0/g/molecular_networking_bug_reports/c/pyQ_rU5g7ps