Exomiser requires (and loads!) tons of genomic data in phenotype-only mode #610
Description
I tried to run Exomiser with the phenotype-only option for an HPO-only phenopacket and was quite confused that it would not run unless I downloaded the 18 GB 2406_hg19.zip file. And indeed, it screened a ClinVar whitelist, included "MVMap 'alleles' opened with 891879779 entries, scored genes, et cetera. WHY? Can't these steps be skipped when there are no variants to be scored?
Thanks,
Dominik
java -jar exomiser-cli-14.1.0.jar --sample test_pp.json --preset phenotype-only
2025-08-28T22:25:07.889+02:00 INFO 32058 --- [ main] o.monarchinitiative.exomiser.cli.Main : Starting Main using Java 22.0.1 with PID 32058 (/opt/exomiser/exomiser-cli-14.1.0.jar started by dominik in /opt/exomiser)
2025-08-28T22:25:08.006+02:00 INFO 32058 --- [ main] o.monarchinitiative.exomiser.cli.Main : No active profile set, falling back to 1 default profile: "default"
2025-08-28T22:25:09.690+02:00 INFO 32058 --- [ main] o.m.exomiser.cli.config.MainConfig : Exomiser home: /opt/exomiser
2025-08-28T22:25:09.710+02:00 INFO 32058 --- [ main] o.m.exomiser.cli.config.MainConfig : Root data source directory set to: /opt/exomiser/data
2025-08-28T22:25:09.717+02:00 INFO 32058 --- [ main] o.m.e.c.g.j.JannovarDataProtoSerialiser : Deserialising Jannovar data from /opt/exomiser/data/2406_hg19/2406_hg19_transcripts_ensembl.ser
2025-08-28T22:25:12.559+02:00 INFO 32058 --- [ main] o.m.e.c.g.j.JannovarDataProtoSerialiser : Deserialisation took 2.841 sec.
2025-08-28T22:25:14.201+02:00 INFO 32058 --- [ main] o.m.e.c.g.dao.ClinVarWhiteListReader : Reading ClinVar whitelist...
2025-08-28T22:25:14.219+02:00 INFO 32058 --- [ main] o.m.e.c.g.dao.serialisers.MvStoreUtil : MVMap 'clinvar' opened with 2897430 entries
2025-08-28T22:25:22.402+02:00 INFO 32058 --- [ main] o.m.e.c.g.dao.ClinVarWhiteListReader : Read 238619 ClinVar whitelist variants in 8200 ms
2025-08-28T22:25:22.514+02:00 INFO 32058 --- [ main] o.m.e.a.genome.GenomeDataSourceLoader : Loaded 238619 whitelist variants
2025-08-28T22:25:22.837+02:00 INFO 32058 --- [ main] o.m.e.c.g.dao.serialisers.MvStoreUtil : MVMap 'alleles' opened with 891879779 entries
2025-08-28T22:25:22.882+02:00 INFO 32058 --- [ main] o.m.e.c.g.dao.serialisers.MvStoreUtil : MVMap 'clinvar' opened with 2897430 entries
2025-08-28T22:25:29.999+02:00 INFO 32058 --- [ main] o.m.e.core.genome.dao.ClinVarDaoMvStore : Created 19074 ClinVar gene stats in 7115 ms
2025-08-28T22:25:30.074+02:00 INFO 32058 --- [ main] com.zaxxer.hikari.HikariDataSource : 2406_hg19_genome - Starting...
2025-08-28T22:25:30.453+02:00 INFO 32058 --- [ main] com.zaxxer.hikari.pool.HikariPool : 2406_hg19_genome - Added connection conn0: url=jdbc:h2:file:/opt/exomiser/data/2406_hg19/2406_hg19_genome user=SA
2025-08-28T22:25:30.456+02:00 INFO 32058 --- [ main] com.zaxxer.hikari.HikariDataSource : 2406_hg19_genome - Start completed.
2025-08-28T22:25:31.745+02:00 INFO 32058 --- [ main] g.GenomeAnalysisServiceAutoConfiguration : Configured hg19 genome analysis service
2025-08-28T22:25:31.846+02:00 INFO 32058 --- [ main] com.zaxxer.hikari.HikariDataSource : 2406_phenotype - Starting...
2025-08-28T22:25:32.108+02:00 INFO 32058 --- [ main] com.zaxxer.hikari.pool.HikariPool : 2406_phenotype - Added connection conn10: url=jdbc:h2:file:/opt/exomiser/data/2406_phenotype/2406_phenotype user=SA
2025-08-28T22:25:32.109+02:00 INFO 32058 --- [ main] com.zaxxer.hikari.HikariDataSource : 2406_phenotype - Start completed.
2025-08-28T22:25:35.243+02:00 INFO 32058 --- [ main] o.m.exomiser.cli.config.MainConfig : Default results directory set to: /opt/exomiser/results
2025-08-28T22:25:35.284+02:00 INFO 32058 --- [ main] o.m.e.a.ExomiserConfigReporter : exomiser.data-directory: /opt/exomiser/data
2025-08-28T22:25:35.285+02:00 INFO 32058 --- [ main] o.m.e.a.ExomiserConfigReporter : exomiser.hg19.data-version: 2406
2025-08-28T22:25:35.285+02:00 INFO 32058 --- [ main] o.m.e.a.ExomiserConfigReporter : exomiser.hg19.clinvar-data-version: 2406
2025-08-28T22:25:35.285+02:00 INFO 32058 --- [ main] o.m.e.a.ExomiserConfigReporter : exomiser.hg38.data-version: -
2025-08-28T22:25:35.285+02:00 INFO 32058 --- [ main] o.m.e.a.ExomiserConfigReporter : exomiser.phenotype.data-version: 2406
2025-08-28T22:25:35.702+02:00 INFO 32058 --- [ main] o.monarchinitiative.exomiser.cli.Main : Started Main in 28.457 seconds (process running for 29.033)
2025-08-28T22:25:35.931+02:00 INFO 32058 --- [ main] o.m.e.cli.ExomiserCommandLineRunner : Exomiser running...
2025-08-28T22:25:35.949+02:00 INFO 32058 --- [ main] o.m.exomiser.core.analysis.JobParser : Running PHENOTYPE_ONLY preset
2025-08-28T22:25:35.954+02:00 INFO 32058 --- [ main] o.m.e.core.analysis.AnalysisStepChecker : CAUTION: Analysis contains no variant filtering steps. This will not perform well.
2025-08-28T22:25:35.960+02:00 INFO 32058 --- [ main] o.m.exomiser.core.Exomiser : Running analysis using hg19 assembly with mode: PASS_ONLY
2025-08-28T22:25:35.969+02:00 INFO 32058 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Validating sample input data
2025-08-28T22:25:35.992+02:00 INFO 32058 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Running analysis for proband patient without VCF
2025-08-28T22:25:36.639+02:00 WARN 32058 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : RUNNING AN ANALYSIS WITHOUT ANY VARIANT FILTERING WILL LEAD TO SUB-OPTIMAL RESULTS!
2025-08-28T22:25:36.653+02:00 INFO 32058 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Checking inheritance mode compatibility with [] for genes which passed filters
2025-08-28T22:25:36.717+02:00 INFO 32058 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Running Prioritiser: OmimPrioritiser{}
2025-08-28T22:25:39.572+02:00 INFO 32058 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Running Prioritiser: HiPhivePriority{options=HiPhiveOptions{diseaseId='', candidateGeneSymbol='', benchmarkingEnabled=false, runPpi=true, runHuman=true, runMouse=true, runFish=true}}
2025-08-28T22:25:53.180+02:00 INFO 32058 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Scoring genes
2025-08-28T22:25:56.028+02:00 INFO 32058 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Analysed sample patient with 34828 genes containing 0 filtered variants
2025-08-28T22:25:56.031+02:00 INFO 32058 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Finished analysis in 0m 20s 38ms (20038 ms)
2025-08-28T22:25:56.031+02:00 INFO 32058 --- [ main] o.m.e.cli.ExomiserCommandLineRunner : Writing results...
2025-08-28T22:26:24.636+02:00 INFO 32058 --- [ main] com.zaxxer.hikari.HikariDataSource : 2406_phenotype - Shutdown initiated...
2025-08-28T22:26:24.646+02:00 INFO 32058 --- [ main] com.zaxxer.hikari.HikariDataSource : 2406_phenotype - Shutdown completed.
2025-08-28T22:26:24.647+02:00 INFO 32058 --- [ main] com.zaxxer.hikari.HikariDataSource : 2406_hg19_genome - Shutdown initiated...
2025-08-28T22:26:24.649+02:00 INFO 32058 --- [ main] com.zaxxer.hikari.HikariDataSource : 2406_hg19_genome - Shutdown completed.
2025-08-28T22:26:24.651+02:00 INFO 32058 --- [ main] o.monarchinitiative.exomiser.cli.Main : Exomising finished - Bye!