search

exomiser / Exomiser

A Tool to Annotate and Prioritize Exome Variants
https://exomiser.readthedocs.io
GNU Affero General Public License v3.0
202 stars 55 forks source link

Results folder empty #404

Open soumyarao86 opened 3 years ago

soumyarao86 commented 3 years ago

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!
soumyarao86 commented 3 years ago 
(/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
julesjacobsen commented 3 years ago

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.