Issue with YAML input

[kyauy]

Dear LIRICAL team,

Thanks for your great work. I wish to try it.

I downloaded the last release of LIRICAL (v1.3.1) and downloaded the needed files through the download command.

I try to use it with the yaml command. I used the yaml provided in example (https://raw.githubusercontent.com/TheJacksonLaboratory/LIRICAL/master/src/test/resources/yaml/simple.yml).

java -jar LIRICAL/LIRICAL.jar yaml -y LIRICAL/patient/simple.yml

I get this error :

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
java.lang.NullPointerException
    at org.monarchinitiative.lirical.output.HtmlTemplate.<init>(HtmlTemplate.java:87)
    at org.monarchinitiative.lirical.output.LiricalTemplate$Builder.buildGenoPhenoHtmlTemplate(LiricalTemplate.java:176)
    at org.monarchinitiative.lirical.cmd.YamlCommand.writeOutput(YamlCommand.java:94)
    at org.monarchinitiative.lirical.cmd.YamlCommand.runPhenotypeOnly(YamlCommand.java:90)
    at org.monarchinitiative.lirical.cmd.YamlCommand.call(YamlCommand.java:163)
    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)

To be noticed : the phenopacket command worked ! java -jar LIRICAL/LIRICAL.jar phenopacket -p LIRICAL/patient/pfeifferNoVcf.json but doesn't provide the entrezgeneid in output.

Do you have any clues of why?

Thanks for your help! Kevin

[pnrobinson]

There were two issues. One was a bug that I have fixed -- updated version is now uploaded. The other was the prefix in your yaml file /work/software/phenotype_software/LIRICAL/LIRICAL/test_20210409 The prefix is intended to be a simple word and not the path to where LIRICAL should write the output. I will need to update the documtation about the YAML file thanks for pointing this out. I will merge everything later today.

[kyauy]

Thanks a lot, Mr Robinson for your answer and this fix. The YAML input works with v1.3.2! In the HPO only mode, can you confirm that we can't have the EntrezGeneID in the prediction? If so, I will use the mim2gene_medgen to get the gene associated. Thanks again!

[yuanxiao1988]

Thanks a lot, Mr Robinson for your answer and this fix. The YAML input works with v1.3.2! In the HPO only mode, can you confirm that we can't have the EntrezGeneID in the prediction? If so, I will use the mim2gene_medgen to get the gene associated. Thanks again!

In my case, the v1.3.2 is still not working in HPO-only mode.

As the same with your case, the EntrezGeneID column of the running result shows all "n/a". I think it means the running is not fully succeeded. This is my error info:

[ERROR]YamlCommand - YamlCommand.javaorg.monarchinitiative.lirical.cmd.YamlCommand.writeOutput(YamlCommand.java:101) - Done analysis of /work/software/phenotype_software/LIRICAL/LIRICAL_new/LIRICAL/test_20210409.html

Dear Prof. Robinson @pnrobinson, please help to check this problem. Thank you very much!

[pnrobinson]

In the phenotype only mode, LIRICAL does not output genes and therefore it write "n/a" (not available). LIRICAL output genes if you use it with a VCF file as input.

[yuanxiao1988]

In the phenotype only mode, LIRICAL does not output genes and therefore it write "n/a" (not available). LIRICAL output genes if you use it with a VCF file as input.

Thank you so much!

[kyauy]

Thanks a lot for these informations!