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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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Exomiser exits without saving any results #342

Closed MartinMJohansson closed 1 year ago

MartinMJohansson commented 5 years ago

Hello,

Newbie to Exomiser but I managed to follow instructions and made suggested changes to the files prior running. I suspect that my main issue is related to memory use since I can make Exomiser to run only partially. Below is the output from Exomiser which shows at what step the software exits, errors when trying to run on recommended memory settings and system info of the PC that I am working on. I have enough of RAM on the machine so I have no idea why it does not accept the original settings.

I would highly appreciate any suggestions that will help the Exomiser to finalize the analysis and save the results to folder.

Regards, Martin

Output from CMD D:\DIS\exomiser\exomiser-cli-11.0.0>java -Xms1048M -Xms1150M -jar exomiser-cli-11.0.0.jar --analysis examples/test-analysis-exome.yml 12:05:55.211 [main] INFO org.monarchinitiative.exomiser.cli.Main - Locale set to en_GB

Welcome to:

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A Tool to Annotate and Prioritize Exome Variants v11.0.0

2019-06-28 12:05:55.534 INFO 17744 --- [ main] org.monarchinitiative.exomiser.cli.Main : Starting Main on Seventeen-PC with PID 17744 (D:\DIS\exomiser\exomiser-cli-11.0.0\exomiser-cli-11.0.0.jar started by DorFP17 in D:\DIS\exomiser\exomiser-cli-11.0.0) 2019-06-28 12:05:55.536 INFO 17744 --- [ main] org.monarchinitiative.exomiser.cli.Main : No active profile set, falling back to default profiles: default 2019-06-28 12:05:55.561 INFO 17744 --- [ main] s.c.a.AnnotationConfigApplicationContext : Refreshing org.springframework.context.annotation.AnnotationConfigApplicationContext@de5251: startup date [Fri Jun 28 12:05:55 EDT 2019]; root of context hierarchy 2019-06-28 12:05:56.083 INFO 17744 --- [ main] o.m.exomiser.cli.config.MainConfig : Exomiser home: D:\DIS\exomiser\exomiser-cli-11.0.0 2019-06-28 12:05:56.092 INFO 17744 --- [ main] o.m.exomiser.cli.config.MainConfig : Exomiser data directory not defined in properties. Checking for default... 2019-06-28 12:05:56.092 INFO 17744 --- [ main] o.m.exomiser.cli.config.MainConfig : Found default data directory: D:\DIS\exomiser\exomiser-cli-11.0.0\data 2019-06-28 12:05:56.104 INFO 17744 --- [ main] com.zaxxer.hikari.HikariDataSource : exomiser-phenotype-1811 - Starting... 2019-06-28 12:05:56.277 INFO 17744 --- [ main] com.zaxxer.hikari.HikariDataSource : exomiser-phenotype-1811 - Start completed. 2019-06-28 12:05:59.759 INFO 17744 --- [ main] com.zaxxer.hikari.HikariDataSource : exomiser-genome-hg19-1811 - Starting... 2019-06-28 12:05:59.764 INFO 17744 --- [ main] com.zaxxer.hikari.HikariDataSource : exomiser-genome-hg19-1811 - Start completed. 2019-06-28 12:05:59.766 INFO 17744 --- [ main] o.m.e.c.g.j.JannovarDataProtoSerialiser : Deserialising Jannovar data from D:\DIS\exomiser\exomiser-cli-11.0.0\data\1811_hg19\1811_hg19_transcripts_ensembl.ser 2019-06-28 12:06:05.387 INFO 17744 --- [ main] o.m.e.c.g.j.JannovarDataProtoSerialiser : Deserialisation took 5.621 sec. 2019-06-28 12:06:12.184 WARN 17744 --- [ main] o.m.e.a.genome.GenomeDataSourceLoader : Data for LOCAL is not configured. THIS WILL LEAD TO ERRORS IF REQUIRED DURING ANALYSIS. Check the application.properties is pointing to a valid file. 2019-06-28 12:06:12.184 WARN 17744 --- [ main] o.m.e.a.genome.GenomeDataSourceLoader : Data for CADD snv is not configured. THIS WILL LEAD TO ERRORS IF REQUIRED DURING ANALYSIS. Check the application.properties is pointing to a valid file. 2019-06-28 12:06:12.185 WARN 17744 --- [ main] o.m.e.a.genome.GenomeDataSourceLoader : Data for CADD InDel is not configured. THIS WILL LEAD TO ERRORS IF REQUIRED DURING ANALYSIS. Check the application.properties is pointing to a valid file. 2019-06-28 12:06:12.185 WARN 17744 --- [ main] o.m.e.a.genome.GenomeDataSourceLoader : Data for REMM is not configured. THIS WILL LEAD TO ERRORS IF REQUIRED DURING ANALYSIS. Check the application.properties is pointing to a valid file. 2019-06-28 12:06:12.335 INFO 17744 --- [ main] g.GenomeAnalysisServiceAutoConfiguration : Configured hg19 genome analysis service 2019-06-28 12:06:12.340 INFO 17744 --- [ main] o.m.exomiser.cli.config.MainConfig : Default results directory set to: D:\DIS\exomiser\exomiser-cli-11.0.0\results 2019-06-28 12:06:12.593 INFO 17744 --- [ main] o.s.j.e.a.AnnotationMBeanExporter : Registering beans for JMX exposure on startup 2019-06-28 12:06:12.594 INFO 17744 --- [ main] o.s.j.e.a.AnnotationMBeanExporter : Bean with name 'phenotypeDataSource' has been autodetected for JMX exposure 2019-06-28 12:06:12.596 INFO 17744 --- [ main] o.s.j.e.a.AnnotationMBeanExporter : Located MBean 'phenotypeDataSource': registering with JMX server as MBean [com.zaxxer.hikari:name=phenotypeDataSource,type=HikariDataSource] 2019-06-28 12:06:12.602 INFO 17744 --- [ main] org.monarchinitiative.exomiser.cli.Main : Started Main in 17.307 seconds (JVM running for 17.506) 2019-06-28 12:06:12.605 INFO 17744 --- [ main] o.m.e.cli.ExomiserCommandLineRunner : Exomiser running... 2019-06-28 12:06:12.650 INFO 17744 --- [ main] o.m.e.core.analysis.AnalysisParser : Made HiPhiveOptions{diseaseId='', candidateGeneSymbol='', benchmarkingEnabled=false, runPpi=true, runHuman=true, runMouse=true, runFish=true} 2019-06-28 12:06:12.657 INFO 17744 --- [ main] o.m.exomiser.core.Exomiser : Running analysis using hg19 assembly with mode: PASS_ONLY 2019-06-28 12:06:12.659 INFO 17744 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Starting analysis 2019-06-28 12:06:12.659 INFO 17744 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Using genome assembly hg19 2019-06-28 12:06:12.659 INFO 17744 --- [ main] o.m.exomiser.core.genome.VcfFiles : Reading VCF header from file examples\Pfeiffer.vcf 2019-06-28 12:06:12.678 INFO 17744 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Checking proband and pedigree for VCF examples\Pfeiffer.vcf 2019-06-28 12:06:12.679 INFO 17744 --- [ main] o.m.e.c.a.util.SampleIdentifierUtil : Proband sample name not specified - using sample name 'manuel' from VCF 2019-06-28 12:06:12.680 INFO 17744 --- [ main] o.m.e.c.a.util.PedigreeSampleValidator : No pedigree provided for sample 'manuel' 2019-06-28 12:06:12.680 INFO 17744 --- [ main] o.m.e.c.a.util.PedigreeSampleValidator : Creating single-sample pedigree for manuel 2019-06-28 12:06:12.687 INFO 17744 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Running analysis for proband manuel (sample 1 in VCF) from samples: [manuel] 2019-06-28 12:06:12.904 INFO 17744 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Filtering variants with: 2019-06-28 12:06:12.905 INFO 17744 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : VariantEffectFilter{offTargetVariantTypes=[CODING_TRANSCRIPT_INTRON_VARIANT, NON_CODING_TRANSCRIPT_EXON_VARIANT, NON_CODING_TRANSCRIPT_INTRON_VARIANT, FIVE_PRIME_UTR_EXON_VARIANT, THREE_PRIME_UTR_EXON_VARIANT, FIVE_PRIME_UTR_INTRON_VARIANT, THREE_PRIME_UTR_INTRON_VARIANT, UPSTREAM_GENE_VARIANT, DOWNSTREAM_GENE_VARIANT, INTERGENIC_VARIANT, REGULATORY_REGION_VARIANT]} 2019-06-28 12:06:12.905 INFO 17744 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : FrequencyFilter{maxFreq=2.0} 2019-06-28 12:06:12.906 INFO 17744 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : PathogenicityFilter{keepNonPathogenic=true} 2019-06-28 12:06:12.906 INFO 17744 --- [ main] o.m.exomiser.core.genome.VcfFiles : Reading variants from VCF file examples\Pfeiffer.vcf 2019-06-28 12:06:12.914 INFO 17744 --- [ main] o.m.e.core.genome.VariantFactoryImpl : Annotating variant records, trimming sequences and normalising positions... 2019-06-28 12:08:20.371 INFO 17744 --- [ main] o.m.e.core.genome.VariantFactoryImpl : Processed 37709 variant records into 37300 single allele variants, 409 are missing annotations, most likely due to non-numeric chromosome designations 2019-06-28 12:08:20.372 INFO 17744 --- [ main] o.m.e.core.genome.VariantFactoryImpl : Variant annotation finished in 2m 7s 457ms (127457 ms) 2019-06-28 12:08:20.372 INFO 17744 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 37709 variants - 681 passed variant filters 2019-06-28 12:08:20.377 INFO 17744 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Checking inheritance mode compatibility with [AUTOSOMAL_DOMINANT, AUTOSOMAL_RECESSIVE, X_RECESSIVE, X_DOMINANT, MITOCHONDRIAL] for genes which passed filters 2019-06-28 12:08:23.763 INFO 17744 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Running GeneFilter: InheritanceFilter{compatibleModes=[AUTOSOMAL_DOMINANT, AUTOSOMAL_RECESSIVE, X_RECESSIVE, X_DOMINANT, MITOCHONDRIAL]} 2019-06-28 12:08:23.804 INFO 17744 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Running Prioritiser: OmimPrioritiser{} 2019-06-28 12:08:28.315 INFO 17744 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Running Prioritiser: HiPhivePriority{options=HiPhiveOptions{diseaseId='', candidateGeneSymbol='', benchmarkingEnabled=false, runPpi=true, runHuman=true, runMouse=true, runFish=true}} 2019-06-28 12:08:47.148 INFO 17744 --- [ main] com.zaxxer.hikari.HikariDataSource : exomiser-phenotype-1811 - Shutdown initiated... 2019-06-28 12:08:47.151 INFO 17744 --- [ main] com.zaxxer.hikari.HikariDataSource : exomiser-phenotype-1811 - Shutdown completed.

D:\DIS\exomiser\exomiser-cli-11.0.0>

Error while running on original memmory setting: D:\DIS\exomiser\exomiser-cli-11.0.0>java -Xms2g -Xmx4g -jar exomiser-cli-11.0.0.jar --analysis examples/test-analysis-exome.yml Invalid maximum heap size: -Xmx4g The specified size exceeds the maximum representable size. Error: Could not create the Java Virtual Machine. Error: A fatal exception has occurred. Program will exit.

I have experimented with various settings and got this one to work: -Xms1048M -Xms1150M

Hardware specifications: Host Name: SE OS Name: Microsoft Windows 10 Pro OS Version: 10.0.16299 N/A Build 16299 OS Manufacturer: Microsoft Corporation OS Configuration: Member Workstation OS Build Type: Multiprocessor Free Registered Owner: N/A Registered Organization: N/A
Original Install Date: 7/26/2018, 1:53:04 PM System Boot Time: 6/18/2019, 7:40:58 AM System Manufacturer: Dell Inc. System Model: OptiPlex 5060 System Type: x64-based PC Processor(s): 1 Processor(s) Installed. [01]: Intel64 Family 6 Model 158 Stepping 10 GenuineIntel ~3192 Mhz BIOS Version: Dell Inc. 1.0.20, 5/24/2018 Windows Directory: C:\Windows System Directory: C:\Windows\system32 Boot Device: \Device\HarddiskVolume1 System Locale: en-us;English (United States) Input Locale: en-us;English (United States) Time Zone: (UTC-05:00) Eastern Time (US & Canada) Total Physical Memory: 32,573 MB Available Physical Memory: 26,003 MB Virtual Memory: Max Size: 37,437 MB Virtual Memory: Available: 30,172 MB Virtual Memory: In Use: 7,265 MB Page File Location(s): C:\pagefile.sys Hyper-V Requirements: VM Monitor Mode Extensions: Yes Virtualization Enabled In Firmware: Yes Second Level Address Translation: Yes Data Execution Prevention Available: Yes

julesjacobsen commented 5 years ago

Hi, sorry this took so long - The JVM reports you're machine doesn't have enough spare RAM to run an analysis using 4GB. You might need to close some other applications or check you're not running this with multiple other users.