Exomiser
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exomiser
exomiser
Results folder empty
Hi, I tested exomiser using the option --analysis examples/test-analysis-exome.yml and it worked. But when I try to test with .vcf file as input, it runs and throws no errors but the results directory is empty. Please correct me if I made a mistake, need to change anything in the command or placing the files and directories.
(/tools/main) [srng3_umsystem_edu@umkc-ds-coxlab-kfe63-compute exomiser-cli-12.1.0]$ java -Xms2g -Xmx4g -jar exomiser-cli-12.1.0.jar -v Pfeiffer.vcf --prioritiser hiphive -I AD -F 1 --hpo-ids HP:0000006,HP:0000174,HP:0000194,HP:0000218,HP:0000238,HP:0000244,HP:0000272,HP:0000303,HP:0000316,HP:0000322,HP:0000324,H P:0000327,HP:0000348,HP:0000431,HP:0000452,HP:0000453,HP:0000470,HP:0000486,HP:0000494,HP:0000508,HP:0000586,HP:0000678,HP:0001156,HP:0001249,HP:0002308,HP:0 002676,HP:0002780,HP:0003041,HP:0003070,HP:0003196,HP:0003272,HP:0003307,HP:0003795,HP:0004209,HP:0004322,HP:0004440,HP:0005048,HP:0005280,HP:0005347,HP:0006 101,HP:0006110,HP:0009602,HP:0009773,HP:0010055,HP:0010669,HP:0011304 -v examples/Pfeiffer.vcf
23:33:54.224 [main] INFO org.monarchinitiative.exomiser.cli.Main - Locale set to en_GB
Welcome to:
_____ _ _____ _
|_ _| |__ ___ | ____|_ _____ _ __ ___ (_)___ ___ _ __
| | | '_ \ / _ \ | _| \ \/ / _ \| '_ ` _ \| / __|/ _ \ '__|
| | | | | | __/ | |___ > < (_) | | | | | | \__ \ __/ |
|_| |_| |_|\___| |_____/_/\_\___/|_| |_| |_|_|___/\___|_|
A Tool to Annotate and Prioritize Exome Variants v12.1.0
2021-08-03 23:33:54.742 INFO 79161 --- [ main] org.monarchinitiative.exomiser.cli.Main : Starting Main on umkc-ds-coxlab-kfe63-compute with PID 7 9161 (/working/exomiser/exomiser-cli-12.1.0/exomiser-cli-12.1.0.jar started by srng3_umsystem_edu in /working/exomiser/exomiser-cli-12.1.0)
2021-08-03 23:33:54.744 INFO 79161 --- [ main] org.monarchinitiative.exomiser.cli.Main : No active profile set, falling back to default profiles: default
2021-08-03 23:33:55.823 INFO 79161 --- [ main] o.m.exomiser.cli.config.MainConfig : Exomiser home: /working/exomiser/exomiser-cli-12.1.0
2021-08-03 23:33:55.840 INFO 79161 --- [ main] o.m.exomiser.cli.config.MainConfig : Exomiser data directory not defined in properties. Check ing for default...
2021-08-03 23:33:55.841 INFO 79161 --- [ main] o.m.exomiser.cli.config.MainConfig : Found default data directory: /working/exomiser/exomiser -cli-12.1.0/data
2021-08-03 23:33:55.853 INFO 79161 --- [ main] com.zaxxer.hikari.HikariDataSource : exomiser-genome-hg19-2102 - Starting...
2021-08-03 23:33:56.078 INFO 79161 --- [ main] com.zaxxer.hikari.HikariDataSource : exomiser-genome-hg19-2102 - Start completed.
2021-08-03 23:33:56.083 INFO 79161 --- [ main] o.m.e.c.g.j.JannovarDataProtoSerialiser : Deserialising Jannovar data from /working/exomiser/exomi ser-cli-12.1.0/data/2102_hg19/2102_hg19_transcripts_ensembl.ser
2021-08-03 23:33:58.091 INFO 79161 --- [ main] o.m.e.c.g.j.JannovarDataProtoSerialiser : Deserialisation took 2.007 sec.
2021-08-03 23:33:58.966 INFO 79161 --- [ main] o.m.e.a.genome.GenomeDataSourceLoader : Loading variant whitelist from: /working/exomiser/exomis er-cli-12.1.0/data/2102_hg19/2102_hg19_clinvar_whitelist.tsv.gz
2021-08-03 23:33:59.193 INFO 79161 --- [ main] o.m.e.a.genome.GenomeDataSourceLoader : Loaded 98379 variants into whitelist
2021-08-03 23:33:59.206 WARN 79161 --- [ main] o.m.e.a.genome.GenomeDataSourceLoader : Data for LOCAL is not configured. THIS WILL LEAD TO ERRO RS IF REQUIRED DURING ANALYSIS. Check the application.properties is pointing to a valid file.
2021-08-03 23:33:59.206 WARN 79161 --- [ main] o.m.e.a.genome.GenomeDataSourceLoader : Data for CADD snv is not configured. THIS WILL LEAD TO E RRORS IF REQUIRED DURING ANALYSIS. Check the application.properties is pointing to a valid file.
2021-08-03 23:33:59.207 WARN 79161 --- [ 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.
2021-08-03 23:33:59.207 WARN 79161 --- [ main] o.m.e.a.genome.GenomeDataSourceLoader : Data for REMM is not configured. THIS WILL LEAD TO ERROR S IF REQUIRED DURING ANALYSIS. Check the application.properties is pointing to a valid file.
2021-08-03 23:33:59.207 WARN 79161 --- [ main] o.m.e.a.genome.GenomeDataSourceLoader : Data for TEST is not configured. THIS WILL LEAD TO ERROR S IF REQUIRED DURING ANALYSIS. Check the application.properties is pointing to a valid file.
2021-08-03 23:33:59.535 INFO 79161 --- [ main] g.GenomeAnalysisServiceAutoConfiguration : Configured hg19 genome analysis service
2021-08-03 23:33:59.557 INFO 79161 --- [ main] com.zaxxer.hikari.HikariDataSource : exomiser-phenotype-2102 - Starting...
2021-08-03 23:33:59.581 INFO 79161 --- [ main] com.zaxxer.hikari.HikariDataSource : exomiser-phenotype-2102 - Start completed.
2021-08-03 23:34:01.266 INFO 79161 --- [ main] o.m.exomiser.cli.config.MainConfig : Default results directory set to: /working/exomiser/exom iser-cli-12.1.0/results
2021-08-03 23:34:02.109 INFO 79161 --- [ main] org.monarchinitiative.exomiser.cli.Main : Started Main in 7.748 seconds (JVM running for 8.055)
2021-08-03 23:34:02.112 INFO 79161 --- [ main] o.m.e.cli.ExomiserCommandLineRunner : Exomiser running...
2021-08-03 23:34:02.118 INFO 79161 --- [ main] com.zaxxer.hikari.HikariDataSource : exomiser-phenotype-2102 - Shutdown initiated...
2021-08-03 23:34:02.126 INFO 79161 --- [ main] com.zaxxer.hikari.HikariDataSource : exomiser-phenotype-2102 - Shutdown completed.
2021-08-03 23:34:02.127 INFO 79161 --- [ main] org.monarchinitiative.exomiser.cli.Main : Exomising finished - Bye!
(/tools/main) [srng3_umsystem_edu@umkc-ds-coxlab-kfe63-compute exomiser-cli-12.1.0]$ ll
total 76
-rw-r--r--. 1 srng3_umsystem_edu coxlab 3422 Aug 3 20:58 application.properties
-rw-r--r--. 1 srng3_umsystem_edu coxlab 3421 Aug 3 20:55 application.properties_original
-rw-r--r--. 1 srng3_umsystem_edu coxlab 13818 Oct 1 2019 CHANGELOG.md
drwxrwsr-x. 4 srng3_umsystem_edu coxlab 4096 Aug 3 19:26 data
drwxr-sr-x. 2 srng3_umsystem_edu coxlab 4096 Oct 1 2019 examples
-rw-r--r--. 1 srng3_umsystem_edu coxlab 15258 Oct 1 2019 exomiser-cli-12.1.0.jar
drwxr-sr-x. 2 srng3_umsystem_edu coxlab 4096 Oct 1 2019 lib
-rw-r--r--. 1 srng3_umsystem_edu coxlab 947 Oct 1 2019 LICENCE.txt
-rw-r--r--. 1 srng3_umsystem_edu coxlab 8450 Oct 1 2019 README.md
drwxrwsr-x. 2 srng3_umsystem_edu coxlab 4096 Aug 3 23:16 results
drwxrwsr-x. 2 srng3_umsystem_edu coxlab 4096 Aug 3 20:58 results_test
You should adapt the examples/test-analysis-exome.yml file and run that using the --analysis option. The commands you're trying to run are from versions <= 6.0.0 and no longer work.
