I think you can download and import a new HMDB SDF file to Progenesis. See if it is something wrong with the old SDF file.

Hi Thomas,

Thanks for the suggestion. I tried downloading and importing a new HMDB SDF file into Progenesis, but unfortunately, I'm still experiencing the same issue. Just to be thorough, I also downloaded an earlier version of the SDF file, but I encountered the same error with that one as well.

You may try another set of data or re-install the software.

Hi Thomas, Thanks for the suggestion and your assistance!

Ihsan Yozgat

The error query bond type=8 in Progenesis QI occurs because the HMDB SDF file contains non-standard “query bonds”, which the software can’t process.

Use an Older HMDB SDF File

Try HMDB 2018 or earlier (no query bonds).

Clean the SDF File with RDKit (Python)

Filter out problematic molecules:

from rdkit import Chem

from rdkit.Chem import SDWriter

supplier = Chem.SDMolSupplier('hmdb.sdf')

writer = SDWriter('hmdb_clean.sdf')

for mol in supplier:

if mol and all(b.GetBondTypeAsDouble() != 0 for b in mol.GetBonds()):

writer.write(mol)

writer.close()

Try to Open Babel (less effective)

obabel input.sdf -O cleaned.sdf --gen3d

Use a Different Database for annotation such as KEGG, ChEBI, or LipidMaps (cleaner formats).