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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
190 stars 54 forks source link

Genomiser is abnormally slow and giving different results in full mode #519

Open lacek opened 9 months ago

lacek commented 9 months ago
docker-compose.yml: ```yml version: '3.2' services: exomiser: image: exomiser/exomiser-cli:13.2.0 user: ${UID}:${GID} environment: - SPRING_CONFIG_LOCATION=/exomiser-data/application.properties - "JDK_JAVA_OPTIONS=-Xmx96g -XX:+UseG1GC -XX:ParallelGCThreads=48" volumes: - /etc/passwd:/etc/passwd:ro - /etc/group:/etc/group:ro - ./runtime:/exomiser - ./runtime/exomiser:/exomiser-data - ./runtime/tmp:/app/classes/results working_dir: /exomiser ```

Command used for FULL mode:

wget -O- https://github.com/exomiser/Exomiser/raw/13.2.0/exomiser-cli/src/main/resources/examples/preset-genome-analysis.yml \
  | sed 's/PASS_ONLY/FULL/' > exomiser/exomiser.genome-analysis.yml

SAMPLE=MPHG002
time docker compose run --rm exomiser --assembly hg38 \
  --vcf tmp/$SAMPLE.norm.vcf.gz --sample input/$SAMPLE.sample.yml --ped input/$SAMPLE.ped \
  --output-directory tmp --output-format VCF,TSV_GENE,TSV_VARIANT --output-filename $SAMPLE.norm-genomiser.full \
  --analysis exomiser/exomiser.genome-analysis.yml

time command shows runtime to be 392m18.554s but exomiser log message shows 27m

log message from FULL mode: ``` NOTE: Picked up JDK_JAVA_OPTIONS: -Xmx96g -XX:+UseG1GC -XX:ParallelGCThreads=48 Welcome to: _____ _ _____ _ |_ _| |__ ___ | ____|_ _____ _ __ ___ (_)___ ___ _ __ | | | '_ \ / _ \ | _| \ \/ / _ \| '_ ` _ \| / __|/ _ \ '__| | | | | | | __/ | |___ > < (_) | | | | | | \__ \ __/ | |_| |_| |_|\___| |_____/_/\_\___/|_| |_| |_|_|___/\___|_| A Tool to Annotate and Prioritize Exome Variants v13.2.0 2023-09-19 19:18:57.529 INFO 1 --- [ main] org.monarchinitiative.exomiser.cli.Main : Starting Main using Java 17.0.6 on e19eff03a825 with PID 1 (/app/classes started by lacek in /exomiser) 2023-09-19 19:18:57.532 INFO 1 --- [ main] org.monarchinitiative.exomiser.cli.Main : No active profile set, falling back to 1 default profile: "default" 2023-09-19 19:18:58.492 INFO 1 --- [ main] o.m.exomiser.cli.config.MainConfig : Exomiser home: /app/classes 2023-09-19 19:18:58.505 INFO 1 --- [ main] o.m.exomiser.cli.config.MainConfig : Root data source directory set to: /exomiser-data 2023-09-19 19:18:58.510 INFO 1 --- [ main] o.m.e.c.g.j.JannovarDataProtoSerialiser : Deserialising Jannovar data from /exomiser-data/2302_hg38/2302_hg38_transcripts_ensembl.ser 2023-09-19 19:18:59.267 INFO 1 --- [ main] o.m.e.c.g.j.JannovarDataProtoSerialiser : Deserialisation took 0.756 sec. 2023-09-19 19:18:59.794 INFO 1 --- [ main] o.m.e.c.g.dao.VariantWhiteListLoader : Loading variant whitelist from: /exomiser-data/2302_hg38/2302_hg38_clinvar_whitelist.tsv.gz 2023-09-19 19:19:00.266 INFO 1 --- [ main] o.m.e.c.g.dao.VariantWhiteListLoader : Loaded 180991 variants into whitelist 2023-09-19 19:19:00.387 INFO 1 --- [ main] o.m.e.a.genome.GenomeDataSourceLoader : Opening REMM data from source: /exomiser-data/remm/ReMM.v0.4.hg38.tsv.gz 2023-09-19 19:19:01.306 INFO 1 --- [ main] g.GenomeAnalysisServiceAutoConfiguration : Configured hg38 genome analysis service 2023-09-19 19:19:03.081 INFO 1 --- [ main] o.m.exomiser.cli.config.MainConfig : Default results directory set to: /app/classes/results 2023-09-19 19:19:03.104 INFO 1 --- [ main] o.m.e.a.ExomiserConfigReporter : exomiser.data-directory: /exomiser-data 2023-09-19 19:19:03.104 INFO 1 --- [ main] o.m.e.a.ExomiserConfigReporter : exomiser.hg19.data-version: - 2023-09-19 19:19:03.104 INFO 1 --- [ main] o.m.e.a.ExomiserConfigReporter : exomiser.hg38.data-version: 2302 2023-09-19 19:19:03.105 INFO 1 --- [ main] o.m.e.a.ExomiserConfigReporter : exomiser.phenotype.data-version: 2302 2023-09-19 19:19:03.290 INFO 1 --- [ main] org.monarchinitiative.exomiser.cli.Main : Started Main in 6.187 seconds (JVM running for 6.615) 2023-09-19 19:19:03.546 INFO 1 --- [ main] o.m.e.cli.ExomiserCommandLineRunner : Exomiser running... 2023-09-19 19:19:03.572 INFO 1 --- [ main] o.m.exomiser.core.Exomiser : Running analysis using hg38 assembly with mode: FULL 2023-09-19 19:19:03.576 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Validating sample input data 2023-09-19 19:19:03.653 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Running analysis for proband MPHG002 (sample 1 in VCF) from samples: [MPHG002, MPHG003, MPHG004]. Using coordinates for genome assembly hg38. 2023-09-19 19:19:03.861 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Running Prioritiser: HiPhivePriority{options=HiPhiveOptions{diseaseId='', candidateGeneSymbol='', benchmarkingEnabled=false, runPpi=true, runHuman=true, runMouse=true, runFish=true}} 2023-09-19 19:19:06.509 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Running GeneFilter: PriorityScoreFilter{priorityType=HIPHIVE_PRIORITY, minPriorityScore=0.5009999871253967} 2023-09-19 19:19:06.584 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Filtering variants with: 2023-09-19 19:19:06.584 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : FailedVariantFilter{} 2023-09-19 19:19:06.584 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : RegulatoryFeatureFilter{} 2023-09-19 19:19:06.585 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : FrequencyFilter{maxFreq=2.0} 2023-09-19 19:19:06.586 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Wrapping FrequencyFilter{maxFreq=2.0} with VariantDataProvider for sources [THOUSAND_GENOMES, TOPMED, UK10K, ESP_AFRICAN_AMERICAN, ESP_EUROPEAN_AMERICAN, ESP_ALL, EXAC_AFRICAN_INC_AFRICAN_AMERICAN, EXAC_AMERICAN, EXAC_EAST_ASIAN, EXAC_FINNISH, EXAC_NON_FINNISH_EUROPEAN, EXAC_OTHER, EXAC_SOUTH_ASIAN, GNOMAD_E_AFR, GNOMAD_E_AMR, GNOMAD_E_EAS, GNOMAD_E_FIN, GNOMAD_E_NFE, GNOMAD_E_OTH, GNOMAD_E_SAS, GNOMAD_G_AFR, GNOMAD_G_AMR, GNOMAD_G_EAS, GNOMAD_G_FIN, GNOMAD_G_NFE, GNOMAD_G_OTH, GNOMAD_G_SAS] 2023-09-19 19:19:06.587 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : PathogenicityFilter{keepNonPathogenic=true} 2023-09-19 19:19:06.587 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Wrapping PathogenicityFilter{keepNonPathogenic=true} with VariantDataProvider for sources [REMM, REVEL, MVP] 2023-09-19 19:19:06.588 INFO 1 --- [ main] o.m.e.core.genome.VariantFactoryImpl : Annotating variant records, trimming sequences and normalising positions... 2023-09-19 19:25:10.889 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 100000 variants - 3205 passed variant filters... 2023-09-19 19:31:14.374 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 200000 variants - 4681 passed variant filters... 2023-09-19 19:37:00.411 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 300000 variants - 7136 passed variant filters... 2023-09-19 19:43:13.593 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 400000 variants - 9037 passed variant filters... 2023-09-19 19:49:15.730 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 500000 variants - 10691 passed variant filters... 2023-09-19 19:55:13.856 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 600000 variants - 12089 passed variant filters... 2023-09-19 20:00:46.913 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 700000 variants - 13630 passed variant filters... 2023-09-19 20:06:52.113 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 800000 variants - 15188 passed variant filters... 2023-09-19 20:13:18.232 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 900000 variants - 17069 passed variant filters... 2023-09-19 20:19:33.048 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 1000000 variants - 18627 passed variant filters... 2023-09-19 20:25:43.194 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 1100000 variants - 20290 passed variant filters... 2023-09-19 20:32:03.180 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 1200000 variants - 22745 passed variant filters... 2023-09-19 20:38:18.166 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 1300000 variants - 24374 passed variant filters... 2023-09-19 20:44:25.360 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 1400000 variants - 25796 passed variant filters... 2023-09-19 20:50:43.747 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 1500000 variants - 26984 passed variant filters... 2023-09-19 20:56:49.823 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 1600000 variants - 28038 passed variant filters... 2023-09-19 21:03:27.492 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 1700000 variants - 29350 passed variant filters... 2023-09-19 21:10:01.458 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 1800000 variants - 30568 passed variant filters... 2023-09-19 21:16:31.590 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 1900000 variants - 31596 passed variant filters... 2023-09-19 21:22:49.298 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 2000000 variants - 32664 passed variant filters... 2023-09-19 21:29:00.808 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 2100000 variants - 33940 passed variant filters... 2023-09-19 21:35:08.728 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 2200000 variants - 35234 passed variant filters... 2023-09-19 21:41:21.512 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 2300000 variants - 36382 passed variant filters... 2023-09-19 21:47:11.551 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 2400000 variants - 38158 passed variant filters... 2023-09-19 21:53:14.065 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 2500000 variants - 39131 passed variant filters... 2023-09-19 21:59:15.378 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 2600000 variants - 40644 passed variant filters... 2023-09-19 22:05:08.678 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 2700000 variants - 41984 passed variant filters... 2023-09-19 22:10:59.474 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 2800000 variants - 43108 passed variant filters... 2023-09-19 22:16:57.052 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 2900000 variants - 45778 passed variant filters... 2023-09-19 22:23:00.655 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 3000000 variants - 49115 passed variant filters... 2023-09-19 22:29:01.228 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 3100000 variants - 50650 passed variant filters... 2023-09-19 22:34:49.961 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 3200000 variants - 51964 passed variant filters... 2023-09-19 22:41:06.301 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 3300000 variants - 53230 passed variant filters... 2023-09-19 22:47:13.243 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 3400000 variants - 54517 passed variant filters... 2023-09-19 22:53:01.366 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 3500000 variants - 56134 passed variant filters... 2023-09-19 22:58:57.094 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 3600000 variants - 57839 passed variant filters... 2023-09-19 23:05:09.052 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 3700000 variants - 59113 passed variant filters... 2023-09-19 23:11:23.800 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 3800000 variants - 61186 passed variant filters... 2023-09-19 23:17:34.763 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 3900000 variants - 62886 passed variant filters... 2023-09-19 23:23:49.830 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 4000000 variants - 64352 passed variant filters... 2023-09-19 23:29:47.183 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 4100000 variants - 65955 passed variant filters... 2023-09-19 23:35:54.722 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 4200000 variants - 67383 passed variant filters... 2023-09-19 23:42:13.743 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 4300000 variants - 69050 passed variant filters... 2023-09-19 23:48:13.899 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 4400000 variants - 70523 passed variant filters... 2023-09-19 23:54:24.794 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 4500000 variants - 72200 passed variant filters... 2023-09-20 00:00:37.400 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 4600000 variants - 73455 passed variant filters... 2023-09-20 00:06:55.947 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 4700000 variants - 73981 passed variant filters... 2023-09-20 00:13:09.331 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 4800000 variants - 75501 passed variant filters... 2023-09-20 00:19:11.719 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 4900000 variants - 77253 passed variant filters... 2023-09-20 00:25:03.277 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 5000000 variants - 78450 passed variant filters... 2023-09-20 00:31:15.330 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 5100000 variants - 80638 passed variant filters... 2023-09-20 00:37:11.462 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 5200000 variants - 82156 passed variant filters... 2023-09-20 00:43:01.422 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 5300000 variants - 83611 passed variant filters... 2023-09-20 00:48:46.426 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 5400000 variants - 86479 passed variant filters... 2023-09-20 00:54:34.924 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 5500000 variants - 88720 passed variant filters... 2023-09-20 01:00:45.860 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 5600000 variants - 90158 passed variant filters... 2023-09-20 01:06:57.315 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 5700000 variants - 91543 passed variant filters... 2023-09-20 01:12:57.479 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 5800000 variants - 93632 passed variant filters... 2023-09-20 01:18:58.325 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 5900000 variants - 96384 passed variant filters... 2023-09-20 01:25:03.918 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 6000000 variants - 97894 passed variant filters... 2023-09-20 01:31:15.520 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 6100000 variants - 99077 passed variant filters... 2023-09-20 01:37:15.256 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 6200000 variants - 101356 passed variant filters... 2023-09-20 01:42:01.720 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 6300000 variants - 102259 passed variant filters... 2023-09-20 01:46:09.718 INFO 1 --- [ main] o.m.e.core.genome.VariantFactoryImpl : Processed 6384761 variant records into 6384761 single allele variants (including 0 structural variants) 2023-09-20 01:46:09.746 INFO 1 --- [ main] o.m.e.core.genome.VariantFactoryImpl : Variant annotation finished in 27m 3s 151ms (23223151 ms) 2023-09-20 01:46:09.747 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 6384761 variants - 103094 passed variant filters 2023-09-20 01:46:16.284 INFO 1 --- [ 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 2023-09-20 01:46:19.384 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Running GeneFilter: InheritanceFilter{compatibleModes=[AUTOSOMAL_DOMINANT, AUTOSOMAL_RECESSIVE, X_RECESSIVE, X_DOMINANT, MITOCHONDRIAL]} 2023-09-20 01:46:20.836 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Running Prioritiser: OmimPrioritiser{} 2023-09-20 01:46:22.564 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Variant filter stats are: 2023-09-20 01:46:22.565 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : PRIORITY_SCORE_FILTER: pass=1492 fail=17540 2023-09-20 01:46:22.565 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : FAILED_VARIANT_FILTER: pass=4422724 fail=0 2023-09-20 01:46:22.565 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : REGULATORY_FEATURE_FILTER: pass=1860557 fail=2562167 2023-09-20 01:46:22.566 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : FREQUENCY_FILTER: pass=330132 fail=4092592 2023-09-20 01:46:22.566 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : PATHOGENICITY_FILTER: pass=4422724 fail=0 2023-09-20 01:46:22.566 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : INHERITANCE_FILTER: pass=6199 fail=4416525 2023-09-20 01:46:27.044 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Scoring genes 2023-09-20 01:46:29.227 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Analysed sample MPHG002 with 18574 genes containing 4422724 filtered variants 2023-09-20 01:46:29.228 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Finished analysis in 27m 25s 574ms (23245574 ms) 2023-09-20 01:46:29.228 INFO 1 --- [ main] o.m.e.cli.ExomiserCommandLineRunner : Writing results... 2023-09-20 01:51:05.115 INFO 1 --- [ main] org.monarchinitiative.exomiser.cli.Main : Exomising finished - Bye! ```

time output:

real    392m18.554s
user    0m4.523s
sys     0m0.659s

On the other hand, using genome preset that does PASS_ONLY mode took only 14m, matching the time 13m 41s measured by exomiser from log message.

Command used for PASS_ONLY mode:

time docker compose run --rm exomiser --assembly hg38 \
  --vcf tmp/$SAMPLE.norm.vcf.gz --sample input/$SAMPLE.sample.yml --ped input/$SAMPLE.ped \
  --output-directory tmp --output-format VCF,TSV_GENE,TSV_VARIANT --output-filename $SAMPLE.norm-genomiser.pass \
  --preset genome
log message from PASS_ONLY mode: ``` NOTE: Picked up JDK_JAVA_OPTIONS: -Xmx96g -XX:+UseG1GC -XX:ParallelGCThreads=48 Welcome to: _____ _ _____ _ |_ _| |__ ___ | ____|_ _____ _ __ ___ (_)___ ___ _ __ | | | '_ \ / _ \ | _| \ \/ / _ \| '_ ` _ \| / __|/ _ \ '__| | | | | | | __/ | |___ > < (_) | | | | | | \__ \ __/ | |_| |_| |_|\___| |_____/_/\_\___/|_| |_| |_|_|___/\___|_| A Tool to Annotate and Prioritize Exome Variants v13.2.0 2023-09-20 10:12:10.770 INFO 1 --- [ main] org.monarchinitiative.exomiser.cli.Main : Starting Main using Java 17.0.6 on ab6b2ea15d53 with PID 1 (/app/classes started by lacek in /exomiser) 2023-09-20 10:12:10.773 INFO 1 --- [ main] org.monarchinitiative.exomiser.cli.Main : No active profile set, falling back to 1 default profile: "default" 2023-09-20 10:12:11.890 INFO 1 --- [ main] o.m.exomiser.cli.config.MainConfig : Exomiser home: /app/classes 2023-09-20 10:12:11.909 INFO 1 --- [ main] o.m.exomiser.cli.config.MainConfig : Root data source directory set to: /exomiser-data 2023-09-20 10:12:11.928 INFO 1 --- [ main] o.m.e.c.g.j.JannovarDataProtoSerialiser : Deserialising Jannovar data from /exomiser-data/2302_hg38/2302_hg38_transcripts_ensembl.ser 2023-09-20 10:12:12.680 INFO 1 --- [ main] o.m.e.c.g.j.JannovarDataProtoSerialiser : Deserialisation took 0.747 sec. 2023-09-20 10:12:13.318 INFO 1 --- [ main] o.m.e.c.g.dao.VariantWhiteListLoader : Loading variant whitelist from: /exomiser-data/2302_hg38/2302_hg38_clinvar_whitelist.tsv.gz 2023-09-20 10:12:13.809 INFO 1 --- [ main] o.m.e.c.g.dao.VariantWhiteListLoader : Loaded 180991 variants into whitelist 2023-09-20 10:12:13.929 INFO 1 --- [ main] o.m.e.a.genome.GenomeDataSourceLoader : Opening REMM data from source: /exomiser-data/remm/ReMM.v0.4.hg38.tsv.gz 2023-09-20 10:12:15.013 INFO 1 --- [ main] g.GenomeAnalysisServiceAutoConfiguration : Configured hg38 genome analysis service 2023-09-20 10:12:17.565 INFO 1 --- [ main] o.m.exomiser.cli.config.MainConfig : Default results directory set to: /app/classes/results 2023-09-20 10:12:17.581 INFO 1 --- [ main] o.m.e.a.ExomiserConfigReporter : exomiser.data-directory: /exomiser-data 2023-09-20 10:12:17.581 INFO 1 --- [ main] o.m.e.a.ExomiserConfigReporter : exomiser.hg19.data-version: - 2023-09-20 10:12:17.581 INFO 1 --- [ main] o.m.e.a.ExomiserConfigReporter : exomiser.hg38.data-version: 2302 2023-09-20 10:12:17.581 INFO 1 --- [ main] o.m.e.a.ExomiserConfigReporter : exomiser.phenotype.data-version: 2302 2023-09-20 10:12:17.791 INFO 1 --- [ main] org.monarchinitiative.exomiser.cli.Main : Started Main in 8.146 seconds (JVM running for 10.519) 2023-09-20 10:12:18.072 INFO 1 --- [ main] o.m.e.cli.ExomiserCommandLineRunner : Exomiser running... 2023-09-20 10:12:18.084 INFO 1 --- [ main] o.m.exomiser.core.analysis.JobParser : Running GENOME preset 2023-09-20 10:12:18.092 INFO 1 --- [ main] o.m.exomiser.core.Exomiser : Running analysis using hg38 assembly with mode: PASS_ONLY 2023-09-20 10:12:18.095 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Validating sample input data 2023-09-20 10:12:18.171 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Running analysis for proband MPHG002 (sample 1 in VCF) from samples: [MPHG002, MPHG003, MPHG004]. Using coordinates for genome assembly hg38. 2023-09-20 10:12:18.342 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Running Prioritiser: HiPhivePriority{options=HiPhiveOptions{diseaseId='', candidateGeneSymbol='', benchmarkingEnabled=false, runPpi=true, runHuman=true, runMouse=true, runFish=true}} 2023-09-20 10:12:21.458 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Running GeneFilter: PriorityScoreFilter{priorityType=HIPHIVE_PRIORITY, minPriorityScore=0.5} 2023-09-20 10:12:21.532 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Filtering variants with: 2023-09-20 10:12:21.532 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : FailedVariantFilter{} 2023-09-20 10:12:21.532 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : RegulatoryFeatureFilter{} 2023-09-20 10:12:21.532 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : FrequencyFilter{maxFreq=2.0} 2023-09-20 10:12:21.534 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Wrapping FrequencyFilter{maxFreq=2.0} with VariantDataProvider for sources [THOUSAND_GENOMES, TOPMED, UK10K, ESP_AFRICAN_AMERICAN, ESP_EUROPEAN_AMERICAN, ESP_ALL, EXAC_AFRICAN_INC_AFRICAN_AMERICAN, EXAC_AMERICAN, EXAC_EAST_ASIAN, EXAC_FINNISH, EXAC_NON_FINNISH_EUROPEAN, EXAC_OTHER, EXAC_SOUTH_ASIAN, GNOMAD_E_AFR, GNOMAD_E_AMR, GNOMAD_E_EAS, GNOMAD_E_FIN, GNOMAD_E_NFE, GNOMAD_E_OTH, GNOMAD_E_SAS, GNOMAD_G_AFR, GNOMAD_G_AMR, GNOMAD_G_EAS, GNOMAD_G_FIN, GNOMAD_G_NFE, GNOMAD_G_OTH, GNOMAD_G_SAS] 2023-09-20 10:12:21.535 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : PathogenicityFilter{keepNonPathogenic=true} 2023-09-20 10:12:21.535 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Wrapping PathogenicityFilter{keepNonPathogenic=true} with VariantDataProvider for sources [REMM, REVEL, MVP] 2023-09-20 10:12:21.536 INFO 1 --- [ main] o.m.e.core.genome.VariantFactoryImpl : Annotating variant records, trimming sequences and normalising positions... 2023-09-20 10:12:39.794 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 100000 variants - 1599 passed variant filters... 2023-09-20 10:12:52.990 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 200000 variants - 2739 passed variant filters... 2023-09-20 10:13:06.528 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 300000 variants - 3899 passed variant filters... 2023-09-20 10:13:21.752 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 400000 variants - 5329 passed variant filters... 2023-09-20 10:13:36.207 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 500000 variants - 6638 passed variant filters... 2023-09-20 10:13:49.676 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 600000 variants - 7810 passed variant filters... 2023-09-20 10:14:00.388 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 700000 variants - 8775 passed variant filters... 2023-09-20 10:14:13.775 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 800000 variants - 9999 passed variant filters... 2023-09-20 10:14:26.803 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 900000 variants - 11453 passed variant filters... 2023-09-20 10:14:41.215 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 1000000 variants - 12801 passed variant filters... 2023-09-20 10:14:55.640 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 1100000 variants - 14104 passed variant filters... 2023-09-20 10:15:09.156 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 1200000 variants - 15546 passed variant filters... 2023-09-20 10:15:21.609 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 1300000 variants - 16781 passed variant filters... 2023-09-20 10:15:32.543 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 1400000 variants - 17811 passed variant filters... 2023-09-20 10:15:43.154 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 1500000 variants - 18738 passed variant filters... 2023-09-20 10:15:52.140 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 1600000 variants - 19437 passed variant filters... 2023-09-20 10:16:02.482 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 1700000 variants - 20404 passed variant filters... 2023-09-20 10:16:13.494 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 1800000 variants - 21398 passed variant filters... 2023-09-20 10:16:21.603 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 1900000 variants - 21981 passed variant filters... 2023-09-20 10:16:31.326 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 2000000 variants - 22762 passed variant filters... 2023-09-20 10:16:40.801 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 2100000 variants - 23610 passed variant filters... 2023-09-20 10:16:51.055 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 2200000 variants - 24544 passed variant filters... 2023-09-20 10:17:01.486 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 2300000 variants - 25416 passed variant filters... 2023-09-20 10:17:13.058 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 2400000 variants - 26594 passed variant filters... 2023-09-20 10:17:23.608 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 2500000 variants - 27422 passed variant filters... 2023-09-20 10:17:35.989 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 2600000 variants - 28591 passed variant filters... 2023-09-20 10:17:45.717 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 2700000 variants - 29469 passed variant filters... 2023-09-20 10:17:54.223 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 2800000 variants - 30242 passed variant filters... 2023-09-20 10:18:08.086 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 2900000 variants - 31554 passed variant filters... 2023-09-20 10:18:28.426 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 3000000 variants - 33613 passed variant filters... 2023-09-20 10:18:41.653 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 3100000 variants - 34646 passed variant filters... 2023-09-20 10:18:52.062 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 3200000 variants - 35462 passed variant filters... 2023-09-20 10:19:02.838 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 3300000 variants - 36388 passed variant filters... 2023-09-20 10:19:13.694 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 3400000 variants - 37323 passed variant filters... 2023-09-20 10:19:23.473 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 3500000 variants - 38220 passed variant filters... 2023-09-20 10:19:36.439 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 3600000 variants - 39319 passed variant filters... 2023-09-20 10:19:46.041 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 3700000 variants - 40106 passed variant filters... 2023-09-20 10:19:59.079 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 3800000 variants - 41304 passed variant filters... 2023-09-20 10:20:11.345 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 3900000 variants - 42571 passed variant filters... 2023-09-20 10:20:24.771 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 4000000 variants - 43724 passed variant filters... 2023-09-20 10:20:38.201 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 4100000 variants - 44984 passed variant filters... 2023-09-20 10:20:50.028 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 4200000 variants - 46034 passed variant filters... 2023-09-20 10:21:03.209 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 4300000 variants - 47263 passed variant filters... 2023-09-20 10:21:14.457 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 4400000 variants - 48351 passed variant filters... 2023-09-20 10:21:29.054 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 4500000 variants - 49597 passed variant filters... 2023-09-20 10:21:40.787 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 4600000 variants - 50574 passed variant filters... 2023-09-20 10:21:46.219 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 4700000 variants - 50908 passed variant filters... 2023-09-20 10:21:58.474 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 4800000 variants - 52021 passed variant filters... 2023-09-20 10:22:12.235 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 4900000 variants - 53270 passed variant filters... 2023-09-20 10:22:23.299 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 5000000 variants - 54145 passed variant filters... 2023-09-20 10:22:38.397 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 5100000 variants - 55641 passed variant filters... 2023-09-20 10:22:49.526 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 5200000 variants - 56723 passed variant filters... 2023-09-20 10:23:01.614 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 5300000 variants - 57838 passed variant filters... 2023-09-20 10:23:21.506 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 5400000 variants - 60109 passed variant filters... 2023-09-20 10:23:38.204 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 5500000 variants - 61835 passed variant filters... 2023-09-20 10:23:49.739 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 5600000 variants - 62871 passed variant filters... 2023-09-20 10:24:02.330 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 5700000 variants - 63913 passed variant filters... 2023-09-20 10:24:16.316 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 5800000 variants - 65260 passed variant filters... 2023-09-20 10:24:30.201 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 5900000 variants - 66796 passed variant filters... 2023-09-20 10:24:41.041 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 6000000 variants - 67827 passed variant filters... 2023-09-20 10:24:49.562 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 6100000 variants - 68469 passed variant filters... 2023-09-20 10:25:04.157 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 6200000 variants - 69892 passed variant filters... 2023-09-20 10:25:12.135 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 6300000 variants - 70517 passed variant filters... 2023-09-20 10:25:17.113 INFO 1 --- [ main] o.m.e.core.genome.VariantFactoryImpl : Processed 6384761 variant records into 6384761 single allele variants (including 0 structural variants) 2023-09-20 10:25:17.114 INFO 1 --- [ main] o.m.e.core.genome.VariantFactoryImpl : Variant annotation finished in 12m 55s 577ms (775577 ms) 2023-09-20 10:25:17.114 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Loaded 6384761 variants - 70906 passed variant filters 2023-09-20 10:25:17.258 INFO 1 --- [ 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 2023-09-20 10:25:54.541 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Running GeneFilter: InheritanceFilter{compatibleModes=[AUTOSOMAL_DOMINANT, AUTOSOMAL_RECESSIVE, X_RECESSIVE, X_DOMINANT, MITOCHONDRIAL]} 2023-09-20 10:25:54.627 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Running Prioritiser: OmimPrioritiser{} 2023-09-20 10:25:55.542 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Variant filter stats are: 2023-09-20 10:25:55.543 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : PRIORITY_SCORE_FILTER: pass=13282 fail=5750 2023-09-20 10:25:55.544 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : FAILED_VARIANT_FILTER: pass=3668044 fail=0 2023-09-20 10:25:55.544 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : REGULATORY_FEATURE_FILTER: pass=1358047 fail=2309997 2023-09-20 10:25:55.544 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : FREQUENCY_FILTER: pass=70906 fail=1287141 2023-09-20 10:25:55.544 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : PATHOGENICITY_FILTER: pass=70906 fail=0 2023-09-20 10:25:55.544 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : INHERITANCE_FILTER: pass=50502 fail=20404 2023-09-20 10:25:57.025 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Scoring genes 2023-09-20 10:25:59.480 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Analysed sample MPHG002 with 6546 genes containing 50502 filtered variants 2023-09-20 10:25:59.481 INFO 1 --- [ main] o.m.e.c.analysis.AbstractAnalysisRunner : Finished analysis in 13m 41s 309ms (821309 ms) 2023-09-20 10:25:59.481 INFO 1 --- [ main] o.m.e.cli.ExomiserCommandLineRunner : Writing results... 2023-09-20 10:26:04.306 INFO 1 --- [ main] org.monarchinitiative.exomiser.cli.Main : Exomising finished - Bye! ```

time output:

real    14m1.786s
user    0m0.289s
sys     0m0.078s

Apart from runtime, the result is also different. For example, in PASS_ONLY mode, a variant can be at rank 290 and AD as mode of inheritance. When in FULL mode, the same variant has rank of 1165 and ANY as mode of inheritance.

julesjacobsen commented 9 months ago

The time log is due to it simply not writing the number of hours taken to the log! So that's a display issue.

Does your variant occur under both AD and ANY when analysed using FULL?

What are you trying to achieve by running on FULL? It will produce a very large and noisy file, plus take much, much longer to run along with consuming a huge amount more RAM as you've discovered.

lacek commented 9 months ago

You are correct about the timing that it's an display issue. The time in ms inside the bracket matches the overall runtime.

Taking variants from chr21, I'm seeing only ANY when using FULL for the previously mentioned example.Below shows the only lines for "21-29888184-C-T" extracted from each of the variants.tsv files. First one from PASS_ONLY and second one from FULL.

#RANK ID GENE_SYMBOL ENTREZ_GENE_ID MOI P-VALUE EXOMISER_GENE_COMBINED_SCORE EXOMISER_GENE_PHENO_SCORE EXOMISER_GENE_VARIANT_SCORE EXOMISER_VARIANT_SCORE CONTRIBUTING_VARIANT WHITELIST_VARIANT VCF_ID RS_ID CONTIG START END REF ALT CHANGE_LENGTH QUAL FILTER GENOTYPE FUNCTIONAL_CLASS HGVS EXOMISER_ACMG_CLASSIFICATION EXOMISER_ACMG_EVIDENCE EXOMISER_ACMG_DISEASE_ID EXOMISER_ACMG_DISEASE_NAME CLINVAR_ALLELE_ID CLINVAR_PRIMARY_INTERPRETATION CLINVAR_STAR_RATING GENE_CONSTRAINT_LOEUF GENE_CONSTRAINT_LOEUF_LOWER GENE_CONSTRAINT_LOEUF_UPPER MAX_FREQ_SOURCE MAX_FREQ ALL_FREQ MAX_PATH_SOURCE MAX_PATH ALL_PATH
290 21-29888184-C-T_AD GRIK1 2897 AD 0.0345 0.6590 0.5000 0.9527 0.0000 0 0 rs448723 rs448723 21 29888184 29888184 C T 0 75.1400 PASS 0 1:0/0:./. coding_transcript_intron_variant GRIK1:ENST00000327783.9:c.118+51199G>A:p.(=) NOT_AVAILABLE NOT_PROVIDED 0 0.50431 0.359 0.72 REMM 0.0 REMM=0.0
1165 21-29888184-C-T_ANY GRIK1 2897 ANY 1.0000 0.0000 0.5000 0.0000 0.0000 0 0 rs448723 rs448723 21 29888184 29888184 C T 0 75.1400 gene-priority 0 1:0/0:./. coding_transcript_intron_variant GRIK1:ENST00000327783.9:c.118+51199G>A:p.(=) NOT_AVAILABLE NOT_PROVIDED 0 0.50431 0.359 0.72 REMM 0.0 REMM=0.0

I'm merely exploring around to see why variants are being filtered.