ielis
commented
5 months ago Hi @dingxm the issue is most likely caused by a bug in the HPO annotation file. We are working on fixing the bug and it will be updated in the next HPO data release.
In the meantime, if you would like to run LIRICAL, you will have to manually download few files and move them into the LIRICAL data directory.
Please go to HPO release v2024-02-08 and look up hp.json and phenotype.hpoa in the release asset section (lower part of the page). You must download these files and move them into your LIRICAL data directory. Based on the logging output above, the data directory is at /data/tools/lirical-cli-2.0.0/data and it should already contain hp.json and phenotype.hpoa. You must overwrite these with the downloaded files.
Then you should be all set for running LIRICAL phenopacket command.
Please give this a try and let me know if the problems persist.
dingxm
I am running the test example and get the error below
base) java -jar /data/tools/lirical-cli-2.0.0/lirical-cli-2.0.0.jar phenopacket -e19 /data/tools/exomiser-cli-14.0.0/data/2402_hg19/2402_hg19_variants.mv.db --assembly hg19 --phenopacket LDS2.v2.json --vcf LDS2.vcf.gz --prefix LDS2 SLF4J(I): Connected with provider of type [ch.qos.logback.classic.spi.LogbackServiceProvider]
| | | | | _/ | / \ | | | | | || |) || | | / \ | | | | | || _ < | | | / | |_ |___||| ___// ____|
LIkelihood Ratio Interpretation of Clinical AbnormaLities :: v2.0.0 ::
10:02:07.481 [main] INFO o.m.l.c.c.LiricalConfigurationCommand - Running LIRICAL from /data/tools/lirical-cli-2.0.0/lirical-cli-2.0.0.jar 10:02:07.486 [main] INFO o.m.l.c.c.LiricalConfigurationCommand - Using data folder at /data/tools/lirical-cli-2.0.0/data 10:02:07.487 [main] INFO o.m.l.c.c.AbstractPrioritizeCommand - Parsing the analysis inputs 10:02:07.728 [main] INFO o.m.l.c.c.AbstractPrioritizeCommand - Bootstrapping LIRICAL java.lang.NullPointerException at java.base/java.util.Objects.requireNonNull(Objects.java:209) at org.monarchinitiative.phenol.annotations.io.hpo.HpoAnnotationLine.(HpoAnnotationLine.java:149)
at org.monarchinitiative.phenol.annotations.io.hpo.HpoAnnotationLine.of(HpoAnnotationLine.java:66)
at org.monarchinitiative.phenol.annotations.io.hpo.HpoAnnotationLine.of(HpoAnnotationLine.java:110)
at org.monarchinitiative.phenol.annotations.io.hpo.HpoaDiseaseDataLoaderDefault.loadDiseaseData(HpoaDiseaseDataLoaderDefault.java:76)
at org.monarchinitiative.phenol.annotations.io.hpo.HpoDiseaseLoaderDefault.load(HpoDiseaseLoaderDefault.java:56)
at org.monarchinitiative.phenol.annotations.io.hpo.HpoDiseaseLoader.load(HpoDiseaseLoader.java:41)
at org.monarchinitiative.lirical.configuration.LoadUtils.loadHpoDiseases(LoadUtils.java:40)
at org.monarchinitiative.lirical.configuration.LiricalBuilder.configurePhenotypeService(LiricalBuilder.java:158)
at org.monarchinitiative.lirical.configuration.LiricalBuilder.build(LiricalBuilder.java:106)
at org.monarchinitiative.lirical.cli.cmd.LiricalConfigurationCommand.bootstrapLirical(LiricalConfigurationCommand.java:208)
at org.monarchinitiative.lirical.cli.cmd.AbstractPrioritizeCommand.execute(AbstractPrioritizeCommand.java:57)
at org.monarchinitiative.lirical.cli.cmd.PhenopacketCommand.execute(PhenopacketCommand.java:15)
at org.monarchinitiative.lirical.cli.cmd.BaseCommand.call(BaseCommand.java:31)
at org.monarchinitiative.lirical.cli.cmd.OutputCommand.call(OutputCommand.java:13)
at org.monarchinitiative.lirical.cli.cmd.BaseCommand.call(BaseCommand.java:18)
at picocli.CommandLine.executeUserObject(CommandLine.java:2041)
at picocli.CommandLine.access$1500(CommandLine.java:148)
at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2461)
at picocli.CommandLine$RunLast.handle(CommandLine.java:2453)
at picocli.CommandLine$RunLast.handle(CommandLine.java:2415)
at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2273)
at picocli.CommandLine$RunLast.execute(CommandLine.java:2417)
at picocli.CommandLine.execute(CommandLine.java:2170)
at org.monarchinitiative.lirical.cli.Main.main(Main.java:46)