Fail: Individual cannot have a null or empty identifier

[antonylebechec]

Dear Exomiser team,

I try to launch exomiser with a family, using a analysis configuration file (including phenopacket section).

In oder to test my code, I use your example "Pfeiffer-quartet.vcf.gz" with your phenopacket "pfieffer-family.yaml", in a analysis.json (try also in yaml format) configuration file (see attached). However, I obtain this fail error below.

Is there a error in my configuration file? Either json or yaml? Do I miss something?

JSON analysis file: analysis.json

YAML analysis file (compressed to be attached): analysis.yaml.zip

Thanks a lot for your help!

Best,

Fail error:

java -XX:ParallelGCThreads=8  -jar /tools/exomiser/13.2.0/bin/exomiser-cli-13.2.0.jar --analysis=/tmp/exomiser/analysis.json --spring.config.location=/databases/exomiser/current/hg19/application.properties --exomiser.data-directory=/databases/exomiser/current/hg19 --exomiser.hg19.transcript-source=refseq

 Welcome to:
  _____ _            _____                     _
 |_   _| |__   ___  | ____|_  _____  _ __ ___ (_)___  ___ _ __
   | | | '_ \ / _ \ |  _| \ \/ / _ \| '_ ` _ \| / __|/ _ \ '__|
   | | | | | |  __/ | |___ >  < (_) | | | | | | \__ \  __/ |
   |_| |_| |_|\___| |_____/_/\_\___/|_| |_| |_|_|___/\___|_|

 A Tool to Annotate and Prioritize Exome Variants     v13.2.0

2023-10-10 13:53:46.971  INFO 13748 --- [           main] org.monarchinitiative.exomiser.cli.Main  : Starting Main using Java 17.0.8 on 3ce9dad51951 with PID 13748 (/tools/exomiser/13.2.0/bin/exomiser-cli-13.2.0.jar started by root in /tools/howard/devel)
2023-10-10 13:53:46.976  INFO 13748 --- [           main] org.monarchinitiative.exomiser.cli.Main  : No active profile set, falling back to 1 default profile: "default"
2023-10-10 13:53:48.356  INFO 13748 --- [           main] o.m.exomiser.cli.config.MainConfig       : Exomiser home: /tools/exomiser/13.2.0/bin
2023-10-10 13:53:48.389  INFO 13748 --- [           main] o.m.exomiser.cli.config.MainConfig       : Root data source directory set to: /databases/exomiser/current/hg19
2023-10-10 13:53:48.396  INFO 13748 --- [           main] o.m.e.c.g.j.JannovarDataProtoSerialiser  : Deserialising Jannovar data from /databases/exomiser/current/hg19/2109_hg19/2109_hg19_transcripts_refseq.ser
2023-10-10 13:53:50.712  INFO 13748 --- [           main] o.m.e.c.g.j.JannovarDataProtoSerialiser  : Deserialisation took 2.315 sec.
2023-10-10 13:53:52.251  INFO 13748 --- [           main] o.m.e.c.g.dao.VariantWhiteListLoader     : Loading variant whitelist from: /databases/exomiser/current/hg19/2109_hg19/2109_hg19_clinvar_whitelist.tsv.gz
2023-10-10 13:53:52.708  INFO 13748 --- [           main] o.m.e.c.g.dao.VariantWhiteListLoader     : Loaded 112258 variants into whitelist
2023-10-10 13:53:53.998  INFO 13748 --- [           main] g.GenomeAnalysisServiceAutoConfiguration : Configured hg19 genome analysis service
2023-10-10 13:53:57.330  INFO 13748 --- [           main] o.m.exomiser.cli.config.MainConfig       : Default results directory set to: /tools/exomiser/13.2.0/bin/results
2023-10-10 13:53:57.351  INFO 13748 --- [           main] o.m.e.a.ExomiserConfigReporter           : exomiser.data-directory: /databases/exomiser/current/hg19
2023-10-10 13:53:57.351  INFO 13748 --- [           main] o.m.e.a.ExomiserConfigReporter           : exomiser.hg19.data-version: 2109
2023-10-10 13:53:57.351  INFO 13748 --- [           main] o.m.e.a.ExomiserConfigReporter           : exomiser.hg38.data-version: -
2023-10-10 13:53:57.352  INFO 13748 --- [           main] o.m.e.a.ExomiserConfigReporter           : exomiser.phenotype.data-version: 2109
2023-10-10 13:53:57.563  INFO 13748 --- [           main] org.monarchinitiative.exomiser.cli.Main  : Started Main in 11.434 seconds (JVM running for 11.899)
2023-10-10 13:53:57.726  INFO 13748 --- [           main] o.m.e.cli.ExomiserCommandLineRunner      : Exomiser running...
2023-10-10 13:53:57.733  INFO 13748 --- [           main] ConditionEvaluationReportLoggingListener :

Error starting ApplicationContext. To display the conditions report re-run your application with 'debug' enabled.
2023-10-10 13:53:57.760 ERROR 13748 --- [           main] o.s.boot.SpringApplication               : Application run failed

java.lang.IllegalStateException: Failed to execute CommandLineRunner
	at org.springframework.boot.SpringApplication.callRunner(SpringApplication.java:771)
	at org.springframework.boot.SpringApplication.callRunners(SpringApplication.java:752)
	at org.springframework.boot.SpringApplication.run(SpringApplication.java:314)
	at org.springframework.boot.SpringApplication.run(SpringApplication.java:1303)
	at org.springframework.boot.SpringApplication.run(SpringApplication.java:1292)
	at org.monarchinitiative.exomiser.cli.Main.main(Main.java:53)
Caused by: java.lang.IllegalArgumentException: Individual cannot have a null or empty identifier
	at org.monarchinitiative.exomiser.core.model.Pedigree$Individual$Builder.id(Pedigree.java:264)
	at org.monarchinitiative.exomiser.core.analysis.sample.PhenopacketPedigreeConverter.createSingleSamplePedigree(PhenopacketPedigreeConverter.java:44)
	at org.monarchinitiative.exomiser.core.analysis.sample.PhenopacketSampleConverter.toExomiserSample(PhenopacketSampleConverter.java:89)
	at org.monarchinitiative.exomiser.core.analysis.sample.PhenopacketConverter.toSample(PhenopacketConverter.java:44)
	at org.monarchinitiative.exomiser.core.analysis.sample.Sample.from(Sample.java:60)
	at org.monarchinitiative.exomiser.core.analysis.JobParser.getSample(JobParser.java:117)
	at org.monarchinitiative.exomiser.core.analysis.JobParser.parseSample(JobParser.java:85)
	at org.monarchinitiative.exomiser.core.analysis.AnalysisParser.parseSample(AnalysisParser.java:99)
	at org.monarchinitiative.exomiser.core.Exomiser.run(Exomiser.java:67)
	at org.monarchinitiative.exomiser.cli.ExomiserCommandLineRunner.runJob(ExomiserCommandLineRunner.java:79)
	at org.monarchinitiative.exomiser.cli.ExomiserCommandLineRunner.runJobs(ExomiserCommandLineRunner.java:62)
	at org.monarchinitiative.exomiser.cli.ExomiserCommandLineRunner.run(ExomiserCommandLineRunner.java:57)
	at org.springframework.boot.SpringApplication.callRunner(SpringApplication.java:768)
	... 5 common frames omitted