Error during GADO prioritisation when it encounters an unexpected HPO term

[Vinícius de Souza]

Description

An experiment that executes GADO prioritisation with these parameters (Note: the file paths are just for example purposes):

Process Command

java -jar GadoCommandline-1.0.1/GADO.jar \
--mode PROCESS \
--output hpoProcessed.txt \
--caseHpo input_cases.txt \
--hpoOntology hp.obo \
--hpoPredictionsInfo predictions_auc_bonf.txt

Prioritise Command

java -jar GadoCommandline-1.0.1/GADO.jar \
--mode PRIORITIZE \
--output results \
--caseHpoProcessed hpoProcessed.txt \
--genes hpo_prediction_genes.txt \
--hpoPredictions genenetwork_bonf_spiked.dat

Error Output

INFO - DEPICT1.0.1
INFO - Current date and time: 2024-05-28 15:56:30
INFO - Supplied options:
INFO -  * Mode: PROCESS
INFO -  * Output: hpoProcessed.txt
INFO -  * Case HPO terms: input_cases.txt
INFO -  * HPO ontology file: hp.obo
INFO -  * Prediction info file: predictions_auc_bonf.txt
INFO - Warning term not found for: HP:0034307 of sample: PMID_10662742_II-1
FATAL - Error: No term named 'HP:0034307'
java.util.NoSuchElementException: No term named 'HP:0034307'
	at org.biojava.nbio.ontology.Ontology$Impl.getTerm(Ontology.java:349)
	at nl.systemsgenetics.gadocommandline.ProcessCaseHpo.process(ProcessCaseHpo.java:104)
	at nl.systemsgenetics.gadocommandline.GadoCommandline.main(GadoCommandline.java:111)

Auxiliar Files

These files were used in the process and prioritisation commands:
input_cases.txt
hpoProcessed.txt

[Patrick Deelen]

I have uploaded the latest version here: https://github.com/molgenis/systemsgenetics/releases/download/GADO_1.0.4/GadoCommandline-1.0.4.tar.gz

Please let met know if the error is also present in this version, then I will have a look at the code

[Vinícius de Souza]

I have uploaded the latest version here: https://github.com/molgenis/systemsgenetics/releases/download/GADO_1.0.4/GadoCommandline-1.0.4.tar.gz

Please let met know if the error is also present in this version, then I will have a look at the code

Unfortunately, the error persists...

[Patrick Deelen]

Debugging is a bit tricky because the line number in your version don't add up to my code base. Could you please run using this snapshot: https://filesender.surf.nl/?s=download&token=a315dd96-6ab1-414a-bb7d-f8e76551756e and then share the output. Then I can see what is going wrong.