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TheJacksonLaboratory / LIRICAL

LIkelihood Ratio Interpretation of Clinical AbnormaLities
https://thejacksonlaboratory.github.io/LIRICAL/stable
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HPO+VCF YAML FILE: Cannot coerce empty String ("") to element of `java.util.LinkedHashMap<java.lang.String,java.lang.String>` #591

Closed Rismail11 closed 1 year ago

Rismail11 commented 1 year ago

Hi LIRICAL Team

I am trying to run lirical 1.3.4 HPO+VCF with a yaml file but I get this error

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance. com.fasterxml.jackson.databind.exc.InvalidFormatException: Cannot coerce empty String ("") to element of java.util.LinkedHashMap<java.lang.String,java.lang.String> (but could if coercion was enabled using CoercionConfig) at [Source: (File); line: 5, column: 10] (through reference chain: org.monarchinitiative.lirical.configuration.YamlConfig["analysis"]) at com.fasterxml.jackson.databind.exc.InvalidFormatException.from(InvalidFormatException.java:67) at com.fasterxml.jackson.databind.DeserializationContext.reportBadCoercion(DeserializationContext.java:1666) at com.fasterxml.jackson.databind.deser.std.StdDeserializer._checkCoercionFail(StdDeserializer.java:1432) at com.fasterxml.jackson.databind.deser.std.StdDeserializer._deserializeFromEmptyString(StdDeserializer.java:325) at com.fasterxml.jackson.databind.deser.std.StdDeserializer._deserializeFromString(StdDeserializer.java:270) at com.fasterxml.jackson.databind.deser.std.MapDeserializer.deserialize(MapDeserializer.java:444) at com.fasterxml.jackson.databind.deser.std.MapDeserializer.deserialize(MapDeserializer.java:32) at com.fasterxml.jackson.databind.deser.impl.MethodProperty.deserializeAndSet(MethodProperty.java:129) at com.fasterxml.jackson.databind.deser.BeanDeserializer.vanillaDeserialize(BeanDeserializer.java:324) at com.fasterxml.jackson.databind.deser.BeanDeserializer.deserialize(BeanDeserializer.java:187) at com.fasterxml.jackson.databind.deser.DefaultDeserializationContext.readRootValue(DefaultDeserializationContext.java:322) at com.fasterxml.jackson.databind.ObjectMapper._readMapAndClose(ObjectMapper.java:4593) at com.fasterxml.jackson.databind.ObjectMapper.readValue(ObjectMapper.java:3413) at org.monarchinitiative.lirical.io.YamlParser.(YamlParser.java:39) at org.monarchinitiative.lirical.cmd.YamlCommand.deYamylate(YamlCommand.java:188) at org.monarchinitiative.lirical.cmd.YamlCommand.call(YamlCommand.java:148) at org.monarchinitiative.lirical.cmd.YamlCommand.call(YamlCommand.java:33) at picocli.CommandLine.executeUserObject(CommandLine.java:1953) at picocli.CommandLine.access$1300(CommandLine.java:145) at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2352) at picocli.CommandLine$RunLast.handle(CommandLine.java:2346) at picocli.CommandLine$RunLast.handle(CommandLine.java:2311) at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) at picocli.CommandLine.execute(CommandLine.java:2078) at org.monarchinitiative.lirical.Lirical.main(Lirical.java:39) org.monarchinitiative.lirical.exception.LiricalRuntimeException: [FATAL] Malformed YAML file: Unrecognized field name in YAML file test.yml. Cannot coerce empty String ("") to element of java.util.LinkedHashMap<java.lang.String,java.lang.String> (but could if coercion was enabled using CoercionConfig) at [Source: (File); line: 5, column: 10] (through reference chain: org.monarchinitiative.lirical.configuration.YamlConfig["analysis"]) at org.monarchinitiative.lirical.io.YamlParser.(YamlParser.java:42) at org.monarchinitiative.lirical.cmd.YamlCommand.deYamylate(YamlCommand.java:188) at org.monarchinitiative.lirical.cmd.YamlCommand.call(YamlCommand.java:148) at org.monarchinitiative.lirical.cmd.YamlCommand.call(YamlCommand.java:33) at picocli.CommandLine.executeUserObject(CommandLine.java:1953) at picocli.CommandLine.access$1300(CommandLine.java:145) at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2352) at picocli.CommandLine$RunLast.handle(CommandLine.java:2346) at picocli.CommandLine$RunLast.handle(CommandLine.java:2311) at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) at picocli.CommandLine.execute(CommandLine.java:2078) at org.monarchinitiative.lirical.Lirical.main(Lirical.java:39)

YAML FILE: analysis: genomeAssembly: hg38 vcf: /users/rismail/lab_work/MSC/OMCA/OMCA_COMPLETE.vcf exomiser: /ilifu/bio/data/exomiser.data/2109_hg38/ datadir: /software/bio/lirical/1.3.4/data/ hpoIds: ['HP:0000478', 'HP:0011304', 'HP:0030084', 'HP:0002194'] prefix: test

My Command: java -jar /software/bio/lirical/1.3.4/LIRICAL.jar yaml -y test.yml

Could you please assist

Thank you in advance!