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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

Exomiser freezes after a few seconds #454

Closed nvadgama87 closed 1 year ago

nvadgama87 commented 1 year ago

Hi there,

I followed the installation instructions and when run Exomiser on the test data, it freezes after the 'Deserialisation took XX secs' step:

 A Tool to Annotate and Prioritize Exome Variants     v13.0.0

2022-10-04 19:56:33.376  INFO 964 --- [           main] org.monarchinitiative.exomiser.cli.Main  : Starting Main using Java 17.0.4 on sh03-08n12.int with PID 964 (/oak/stanford/groups/caseyg21/Nirmal/Exomiser/exomiser-cli-13.0.0/exomiser-cli-13.0.0.jar started by nvadgama in /oak/stanford/groups/caseyg21/Nirmal/Exomiser/exomiser-cli-13.0.0)
2022-10-04 19:56:33.378  INFO 964 --- [           main] org.monarchinitiative.exomiser.cli.Main  : No active profile set, falling back to default profiles: default
2022-10-04 19:56:33.877  INFO 964 --- [           main] o.m.exomiser.cli.config.MainConfig       : Exomiser home: /oak/stanford/groups/caseyg21/Nirmal/Exomiser/exomiser-cli-13.0.0
2022-10-04 19:56:33.883  INFO 964 --- [           main] o.m.exomiser.cli.config.MainConfig       : Data source directory defined in properties as: /oak/stanford/groups/caseyg21/Nirmal/Exomiser/exomiser-cli-13.0.0/data/exomiser-data
2022-10-04 19:56:33.884  INFO 964 --- [           main] o.m.exomiser.cli.config.MainConfig       : Root data source directory set to: /oak/stanford/groups/caseyg21/Nirmal/Exomiser/exomiser-cli-13.0.0/data/exomiser-data
2022-10-04 19:56:33.886  INFO 964 --- [           main] o.m.e.c.g.j.JannovarDataProtoSerialiser  : Deserialising Jannovar data from /oak/stanford/groups/caseyg21/Nirmal/Exomiser/exomiser-cli-13.0.0/data/exomiser-data/2109_hg19/2109_hg19_transcripts_ucsc.ser
2022-10-04 19:56:34.999  INFO 964 --- [           main] o.m.e.c.g.j.JannovarDataProtoSerialiser  : Deserialisation took 1.112 sec.

I ran the command: