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exomiser / Exomiser

A Tool to Annotate and Prioritize Exome Variants
https://exomiser.readthedocs.io
GNU Affero General Public License v3.0
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multi-proband in multi-VCFs #431

Open luceamso opened 2 years ago

luceamso commented 2 years ago

Hi,

My family consists of unaffected parents and 3 affected siblings. It works fine when I specify the proband ID and see each proband one by one, but when I try it to multi, it doesn't work. I've tried several attempts to see the results of all three, but I got the following error message:

java.lang.IllegalStateException: Failed to execute CommandLineRunner
    at org.springframework.boot.SpringApplication.callRunner(SpringApplication.java:794)
    at org.springframework.boot.SpringApplication.callRunners(SpringApplication.java:775)
    at org.springframework.boot.SpringApplication.run(SpringApplication.java:345)
    at org.springframework.boot.SpringApplication.run(SpringApplication.java:1343)
    at org.springframework.boot.SpringApplication.run(SpringApplication.java:1332)
    at org.monarchinitiative.exomiser.cli.Main.main(Main.java:52)
Caused by: java.lang.IllegalArgumentException: Unable to parse job from file examples/cs-fam1-genome-analysis-revel-mvp-remm.yml please check the format.
    at org.monarchinitiative.exomiser.core.analysis.JobReader.parseJob(JobReader.java:87)
    at org.monarchinitiative.exomiser.core.analysis.JobReader.readJob(JobReader.java:74)
    at org.monarchinitiative.exomiser.cli.CommandLineJobReader.readJobs(CommandLineJobReader.java:68)
    at org.monarchinitiative.exomiser.cli.ExomiserCommandLineRunner.run(ExomiserCommandLineRunner.java:55)
    at org.springframework.boot.SpringApplication.callRunner(SpringApplication.java:791)
    ... 5 common frames omitted
Caused by: org.monarchinitiative.exomiser.core.proto.ProtoParser$ProtoParserException: Unable to parse message type org.monarchinitiative.exomiser.api.v1.JobProto$Job from file examples/cs-fam1-genome-analysis-revel-mvp-remm.yml
    at org.monarchinitiative.exomiser.core.proto.ProtoParser.parseFromJsonOrYaml(ProtoParser.java:60)
    at org.monarchinitiative.exomiser.core.analysis.JobReader.parseJob(JobReader.java:81)
    ... 9 common frames omitted
Caused by: com.google.protobuf.InvalidProtocolBufferException: null
    at com.google.protobuf.util.JsonFormat$ParserImpl.merge(JsonFormat.java:1343)
    at com.google.protobuf.util.JsonFormat$Parser.merge(JsonFormat.java:476)
    at org.monarchinitiative.exomiser.core.proto.ProtoParser.parseYaml(ProtoParser.java:86)
    at org.monarchinitiative.exomiser.core.proto.ProtoParser.parseFromJsonOrYaml(ProtoParser.java:56)
    ... 10 common frames omitted

or

java.lang.IllegalStateException: Failed to execute CommandLineRunner
    at org.springframework.boot.SpringApplication.callRunner(SpringApplication.java:794)
    at org.springframework.boot.SpringApplication.callRunners(SpringApplication.java:775)
    at org.springframework.boot.SpringApplication.run(SpringApplication.java:345)
    at org.springframework.boot.SpringApplication.run(SpringApplication.java:1343)
    at org.springframework.boot.SpringApplication.run(SpringApplication.java:1332)
    at org.monarchinitiative.exomiser.cli.Main.main(Main.java:52)
Caused by: java.lang.IllegalArgumentException: Proband '' not present in pedigree
    at org.monarchinitiative.exomiser.core.analysis.sample.Sample.checkSex(Sample.java:84)
    at org.monarchinitiative.exomiser.core.analysis.sample.Sample.<init>(Sample.java:73)
    at org.monarchinitiative.exomiser.core.analysis.sample.Sample$Builder.build(Sample.java:226)
    at org.monarchinitiative.exomiser.core.analysis.sample.SampleProtoConverter.toDomain(SampleProtoConverter.java:75)
    at org.monarchinitiative.exomiser.core.analysis.sample.Sample.from(Sample.java:65)
    at org.monarchinitiative.exomiser.core.analysis.JobParser.getSample(JobParser.java:114)
    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:791)
    ... 5 common frames omitted

I'm working with this pedigree:

#family_ID  sample_ID   paternal_ID maternal_ID sex affect
fam1    F9  0   0   2   1
fam1    F7  0   0   1   1
fam1    F14 F7  F9  2   2
fam1    F8  F7  F9  2   2
fam1    F15 F7  F9  1   2

Is there any way I can see the results of all three? I would highly appreciate if you could have a look. Thank you so much! Seoon

luceamso commented 2 years ago

@julesjacobsen Hi,

I have additional questions. My VCF file (cs_affected_fam.vcf.gz) was annotated with ANNOVAR databases including several customized ones, for instance, “gnomAD_r2.1.1_merged_all” and “bravo_freeze8” etc. So I would like to see the result of variants that follow the frequency of these databases. Is there any way to apply the filter frequency using these customized databases? Thanks again for your time.