pnrobinson
commented
5 years ago There was an inconsistency in the phenotype.hpoa file.
The first lines need to be
#description: HPO annotations for rare diseases [7376: OMIM; 47: DECIPHER; 3300 ORPHANET]
#date: 2019-01-02
#tracker: https://github.com/obophenotype/human-phenotype-ontology
#HPO-version: http://purl.obolibrary.org/obo/hp/releases/2018-12-21/hp.owl
DatabaseID DiseaseName Qualifier HPO_ID Reference Evidence Onset Frequency Sex Modifier Aspect Biocuration
OMIM:216300 CLEFT PALATE, DEAFNESS, AND OLIGODONTIA HP:0000007 OMIM:216300 IEA I HPO:iea[2009-02-17]Probably this should work if you remove the data directory and download everything again. Otherwise you may need to modify the first line (remove #)
Hi Peter,
I am getting an error message when I run the "simulate" command:
objc[46063]: Class JavaLaunchHelper is implemented in both /Library/Java/JavaVirtualMachines/jdk1.8.0_91.jdk/Contents/Home/bin/java (0x10af514c0) and /Library/Java/JavaVirtualMachines/jdk1.8.0_91.jdk/Contents/Home/jre/lib/libinstrument.dylib (0x10c7ad4e0). One of the two will be used. Which one is undefined. org.monarchinitiative.lr2pg.exception.Lr2pgException: Could not parse annotation file: Expected header field 0 to be DatabaseID but got OMIM:210100
at org.monarchinitiative.lr2pg.configuration.Lr2PgFactory.diseaseMap(Lr2PgFactory.java:259) at org.monarchinitiative.lr2pg.cmd.SimulatePhenotypesCommand.run(SimulatePhenotypesCommand.java:59) LRPG: Elapsed time was 7.335 seconds. at org.monarchinitiative.lr2pg.LR2PG.main(LR2PG.java:113)
Could you please check if you get the same error or not? Thank you!