update to HMDB 5.0 gives error with Holmium

So I updated the HMDB for the AccurateMassSearch node of OpenMS to the last version. However, I tried to use it on some mzml files and I got the error below.

ERROR AccurateMassSearch 0:878 Failing process stdout: [File ‘/home/ubuntu/.OpenMS/OpenMS.ini’ is deprecated., Updating missing/wrong entries in ‘/home/kostas/.OpenMS/OpenMS.ini’ with defaults!, Read 22555 entries from mapping file!, Read 33 entries from adduct file ‘/home/kostas/knimestuff/databases/PositiveAdducts.tsv’., Read 15 entries from adduct file ‘/home/kostas/knimestuff/databases/NegativeAdducts.tsv’., Error: Unable to read file (‘Ho’ found. Please use only valid element identifiers or modify share/OpenMS/CHEMISTRY/Elements.xml! in: Unknown element ‘Ho’)]
ERROR AccurateMassSearch 0:878 Failing process stderr:
ERROR AccurateMassSearch 0:878 Return code: 3
ERROR AccurateMassSearch 0:878 Execute failed: Failed to execute node AccurateMassSearch
ERROR DB Connector 0:644 Unable to save internals:

It seems there is a Ho(lmium) element in the new HMDBMappingFile.tsv that does not exist in the Elements.xml. I am using OpenMS 2.6.0 and KNIME 4.1.1 and an update is not very possible right now. So I am wondering, would it be right to somehow add it manually to the Elements.xml or is there something else I can do? Is it possible that other elements are also missing from Elements.xml?

A weird thing is happening. I added manually the elements for which the AccurateMassSearch node was complaining about: Europium, Dysprosium, Holmium, Erbium, Thulium, Lutetium, Osmium and Iridium. But now I get an other error from FeatureFinderMetabo which looks like it is a memory error! The FeatureFinderMetabo Error output says:

*** Error in `/home/kostas/knime_4.1.1/plugins/de.openms.linux.x86_64_2.6.0.202009301213/payload/bin/FeatureFinderMetabo’: free(): invalid next size (fast): 0x00000000085b9d20 ***
(and then the backtrace)

Can some of the isotopes I added cause memory errors? Also, what I noticed, if I remove the last isotope “Iridium” then I get an error at the MapAlignerPoseClustering node about an invalid character at the produced .featureXML file! How is this possible, but most importantly, what is happening? Any ideas?


Yes, some elements are missing in OpenMS 2.6.
See Add missing elements by JangJang3 · Pull Request #5451 · OpenMS/OpenMS · GitHub
Can you try with 2.7?

Yes, fiddling with Element.xml incorrectly can lead to memory errors. I would need to see your changes.

For the featureXML file, I don’t know. I probably would need to see the file. But with memory errors being possible you cannot guarantee for anything anyway.

Thank you very much for your answer! So the elements I ended up adding at the end of the Elements.xml file are Europium, Dysprosium, Holmium, Erbium, Thulium, Lutetium, Osmium, Iridium, Francium and Curium. The file is Elements.xml (69.5 KB).

Regarding the processing, the weird thing is that sometimes I was getting errors at the FeatureFinderMetabo and some other times at the MapAlignerPoseClustering with invalid character. For example, an error of the MapAlignerPoseClustering node is:

/home/jenkins/ws/openms/RC/openms_release_packaging/fd57e9df/source/src/openms/source/FORMAT/HANDLERS/XMLHandler.cpp(107): While loading ‘/tmp/knime_default_hmdb38361/fs-ZipLo_0-674-38395/000/000/3_1_FeatureFinderMetabo_0/20_Rep1_POS.featureXML’: invalid character 0x16 in attribute value ‘x’( in line 3035255 column 21)

and after searching the specific line I got: