[go: nahoru, domu]
Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

multi-proband in multi-VCFs #431

Open
luceamso opened this issue Apr 1, 2022 · 1 comment
Open

multi-proband in multi-VCFs #431

luceamso opened this issue Apr 1, 2022 · 1 comment

Comments

@luceamso
Copy link
luceamso commented Apr 1, 2022 •
edited
Loading

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
Copy link
Author
luceamso commented Apr 18, 2022 •
edited
Loading

@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.

@luceamso luceamso mentioned this issue Apr 19, 2022
Closed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
1 participant
@luceamso