{"action":"created","issue":{"url":"https://api.github.com/repos/broadinstitute/gatk/issues/4975","repository_url":"https://api.github.com/repos/broadinstitute/gatk","labels_url":"https://api.github.com/repos/broadinstitute/gatk/issues/4975/labels{/name}","comments_url":"https://api.github.com/repos/broadinstitute/gatk/issues/4975/comments","events_url":"https://api.github.com/repos/broadinstitute/gatk/issues/4975/events","html_url":"https://github.com/broadinstitute/gatk/issues/4975","id":337548071,"node_id":"MDU6SXNzdWUzMzc1NDgwNzE=","number":4975,"title":"New qual parameter errors GenotypeGVCFs using GenomicsDB database in v4.0.5.0.","user":{"login":"sooheelee","id":11543866,"node_id":"MDQ6VXNlcjExNTQzODY2","avatar_url":"https://avatars2.githubusercontent.com/u/11543866?v=4","gravatar_id":"","url":"https://api.github.com/users/sooheelee","html_url":"https://github.com/sooheelee","followers_url":"https://api.github.com/users/sooheelee/followers","following_url":"https://api.github.com/users/sooheelee/following{/other_user}","gists_url":"https://api.github.com/users/sooheelee/gists{/gist_id}","starred_url":"https://api.github.com/users/sooheelee/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sooheelee/subscriptions","organizations_url":"https://api.github.com/users/sooheelee/orgs","repos_url":"https://api.github.com/users/sooheelee/repos","events_url":"https://api.github.com/users/sooheelee/events{/privacy}","received_events_url":"https://api.github.com/users/sooheelee/received_events","type":"User","site_admin":false},"labels":[{"id":244151192,"node_id":"MDU6TGFiZWwyNDQxNTExOTI=","url":"https://api.github.com/repos/broadinstitute/gatk/labels/Vanilla","name":"Vanilla","color":"ededed","default":false},{"id":153552584,"node_id":"MDU6TGFiZWwxNTM1NTI1ODQ=","url":"https://api.github.com/repos/broadinstitute/gatk/labels/bug","name":"bug","color":"fc2929","default":true}],"state":"open","locked":false,"assignee":{"login":"davidbenjamin","id":8438890,"node_id":"MDQ6VXNlcjg0Mzg4OTA=","avatar_url":"https://avatars3.githubusercontent.com/u/8438890?v=4","gravatar_id":"","url":"https://api.github.com/users/davidbenjamin","html_url":"https://github.com/davidbenjamin","followers_url":"https://api.github.com/users/davidbenjamin/followers","following_url":"https://api.github.com/users/davidbenjamin/following{/other_user}","gists_url":"https://api.github.com/users/davidbenjamin/gists{/gist_id}","starred_url":"https://api.github.com/users/davidbenjamin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/davidbenjamin/subscriptions","organizations_url":"https://api.github.com/users/davidbenjamin/orgs","repos_url":"https://api.github.com/users/davidbenjamin/repos","events_url":"https://api.github.com/users/davidbenjamin/events{/privacy}","received_events_url":"https://api.github.com/users/davidbenjamin/received_events","type":"User","site_admin":false},"assignees":[{"login":"davidbenjamin","id":8438890,"node_id":"MDQ6VXNlcjg0Mzg4OTA=","avatar_url":"https://avatars3.githubusercontent.com/u/8438890?v=4","gravatar_id":"","url":"https://api.github.com/users/davidbenjamin","html_url":"https://github.com/davidbenjamin","followers_url":"https://api.github.com/users/davidbenjamin/followers","following_url":"https://api.github.com/users/davidbenjamin/following{/other_user}","gists_url":"https://api.github.com/users/davidbenjamin/gists{/gist_id}","starred_url":"https://api.github.com/users/davidbenjamin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/davidbenjamin/subscriptions","organizations_url":"https://api.github.com/users/davidbenjamin/orgs","repos_url":"https://api.github.com/users/davidbenjamin/repos","events_url":"https://api.github.com/users/davidbenjamin/events{/privacy}","received_events_url":"https://api.github.com/users/davidbenjamin/received_events","type":"User","site_admin":false}],"milestone":null,"comments":5,"created_at":"2018-07-02T14:42:38Z","updated_at":"2018-07-03T14:50:50Z","closed_at":null,"author_association":"CONTRIBUTOR","body":"Researcher reports error in GenotypeGVCFs that uses a GenomicsDB database using v4.0.5.0. Removing `new qual` param OR using v4.0.4.0 allows the command to run without error.\r\n\r\nI saw a similar error with v4.0.5.1 when I tried to add `new qual` to a workshop hands-on tutorial GenotypeGVCFs step using a GenomicsDB database.\r\n\r\n---\r\nHi,\r\n\r\nI am trying to process locally 260 WES gvcf through joint discovery wdl pipeline. I encountered an error at GenotypeGVCFs below which I am not sure how to proceed.\r\n\r\nI have used all the default reference libraries and only modified the merge_count in the script to be 8144 so that my server resources won't be maxout fully in the ImportGVCFs step. \r\n\r\n[https://github.com/gatk-workflows/gatk4-germline-snps-indels/blob/master/joint-discovery-gatk4-local.wdl](https://github.com/gatk-workflows/gatk4-germline-snps-indels/blob/master/joint-discovery-gatk4-local.wdl \"https://github.com/gatk-workflows/gatk4-germline-snps-indels/blob/master/joint-discovery-gatk4-local.wdl\")\r\n\r\n```\r\n23:17:43.992 WARN  InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples\r\n23:17:44.064 WARN  InbreedingCoeff - Annotation will not be calculated, must provide at least 10 samples\r\n23:17:46.334 INFO  GenotypeGVCFs - Shutting down engine\r\nGENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),30.197597194999727,Cpu time(s),28.791204838999864\r\n[June 25, 2018 11:17:46 PM UTC] org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs done. Elapsed time: 4.01 minutes.\r\nRuntime.totalMemory()=5354029056\r\njava.lang.IllegalArgumentException: log10LikelihoodsOfAC are bad 2.559797571100845E-21,NaN\r\n\tat org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc.AFCalculationResult.<init>(AFCalculationResult.java:72)\r\n\tat org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc.AlleleFrequencyCalculator.getLog10PNonRef(AlleleFrequencyCalculator.java:143)\r\n\tat org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingEngine.calculateGenotypes(GenotypingEngine.java:255)\r\n\tat org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingEngine.calculateGenotypes(GenotypingEngine.java:210)\r\n\tat org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs.calculateGenotypes(GenotypeGVCFs.java:266)\r\n\tat org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs.regenotypeVC(GenotypeGVCFs.java:222)\r\n\tat org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs.apply(GenotypeGVCFs.java:201)\r\n\tat org.broadinstitute.hellbender.engine.VariantWalkerBase.lambda$traverse$0(VariantWalkerBase.java:109)\r\n\tat java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:184)\r\n\tat java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175)\r\n\tat java.util.Iterator.forEachRemaining(Iterator.java:116)\r\n\tat java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)\r\n\tat java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)\r\n\tat java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)\r\n\tat java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:151)\r\n\tat java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:174)\r\n\tat java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)\r\n\tat java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:418)\r\n\tat org.broadinstitute.hellbender.engine.VariantWalkerBase.traverse(VariantWalkerBase.java:107)\r\n\tat org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:980)\r\n\tat org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:135)\r\n\tat org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:180)\r\n\tat org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:199)\r\n\tat org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)\r\n\tat org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)\r\n\tat org.broadinstitute.hellbender.Main.main(Main.java:289)\r\nUsing GATK jar /gatk/build/libs/gatk-package-4.0.5.0-local.jar\r\nRunning:\r\n    java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx5g -Xms5g -jar /gatk/build/libs/gatk-package-4.0.5.0-local.jar GenotypeGVCFs -R /cromwell-executions/JointGenotyping/3a733624-60a0-4e57-b7f5-7b7e99795738/call-GenotypeGVCFs/shard-25/inputs/data1/bill/pipeline/cromwell/hg38/Homo_sapiens_assembly38.fasta -O output.vcf.gz -D /cromwell-executions/JointGenotyping/3a733624-60a0-4e57-b7f5-7b7e99795738/call-GenotypeGVCFs/shard-25/inputs/data1/bill/pipeline/cromwell/hg38/Homo_sapiens_assembly38.dbsnp138.vcf -G StandardAnnotation --only-output-calls-starting-in-intervals --use-new-qual-calculator -V gendb://genomicsdb -L chrY:10821870-11717714\r\n```\r\nThis Issue was generated from your [forums] \r\n[forums]: https://gatkforums.broadinstitute.org/gatk/discussion/12283/running-260-wes-samples-through-joint-discovery-and-vqsr/p1\r\n"},"comment":{"url":"https://api.github.com/repos/broadinstitute/gatk/issues/comments/402184817","html_url":"https://github.com/broadinstitute/gatk/issues/4975#issuecomment-402184817","issue_url":"https://api.github.com/repos/broadinstitute/gatk/issues/4975","id":402184817,"node_id":"MDEyOklzc3VlQ29tbWVudDQwMjE4NDgxNw==","user":{"login":"droazen","id":798637,"node_id":"MDQ6VXNlcjc5ODYzNw==","avatar_url":"https://avatars0.githubusercontent.com/u/798637?v=4","gravatar_id":"","url":"https://api.github.com/users/droazen","html_url":"https://github.com/droazen","followers_url":"https://api.github.com/users/droazen/followers","following_url":"https://api.github.com/users/droazen/following{/other_user}","gists_url":"https://api.github.com/users/droazen/gists{/gist_id}","starred_url":"https://api.github.com/users/droazen/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/droazen/subscriptions","organizations_url":"https://api.github.com/users/droazen/orgs","repos_url":"https://api.github.com/users/droazen/repos","events_url":"https://api.github.com/users/droazen/events{/privacy}","received_events_url":"https://api.github.com/users/droazen/received_events","type":"User","site_admin":false},"created_at":"2018-07-03T14:50:49Z","updated_at":"2018-07-03T14:50:49Z","author_association":"COLLABORATOR","body":"@davidbenjamin The error is not specific to GenomicsDB. @V-Z got the same error with a VCF as input (see https://github.com/broadinstitute/gatk/issues/4544#issuecomment-401904928), so that should make it slightly easier to replicate."}}
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