Unable to deserialise data

[lt11]

Dear authors,

After installing exomiser (14.0.0) on a linux system I get the following error when I run the test (https://exomiser.readthedocs.io/en/latest/installation.html):

2024-09-27T16:39:21.949+02:00  INFO 117413 --- [           main] o.m.e.c.g.j.JannovarDataProtoSerialiser  : Deserialising Jannovar data from /home/ltattini/tools/exomiser/exomiser-cli-14.0.0/${exomiser.data-directory}/2402_hg19/2402_hg19_transcripts_ensembl.ser
2024-09-27T16:39:21.949+02:00 ERROR 117413 --- [           main] o.m.e.c.g.j.JannovarDataProtoSerialiser  : Unable to deserialise data

The 2402_hg19_transcripts_ensembl.ser file is acutally there but it seems the path to it is not correctly reconstructed because of the variable ${exomiser.data-directory}. Did I miss something in the installation process?

[julesjacobsen]

What is the value of the exomiser.data-directory in your application.properties file? If you set it to use the full system path of where you extracted all your data it should work. e.g. exomiser.data-directory=/home/ltattini/tools/exomiser/exomiser-cli-14.0.0 assuming that is where the directory 2402_hg19 is located.

Also, make sure you are using the 2406 data as this has the fixed gnomAD v4.1 allele frequencies - see here: https://github.com/exomiser/Exomiser/discussions/562

[lt11]

Thanks a lot for the prompt reply. The line defining exomiser.data-directory was commented. Removing the comment and setting it as you suggested solved the issue.

Unfortunately I encountered another one still running the test.

2024-09-27T16:26:46.242Z  INFO 1740148 --- [           main] o.m.e.c.g.j.JannovarDataProtoSerialiser  : Deserialising Jannovar data from /data/ssd/lorenzot/exomiser/exomiser-cli-14.0.0/data/2402_hg19/2402_hg19_transcripts_ensembl.ser
2024-09-27T16:26:47.360Z  INFO 1740148 --- [           main] o.m.e.c.g.j.JannovarDataProtoSerialiser  : Deserialisation took 1.117 sec.
2024-09-27T16:26:48.194Z  INFO 1740148 --- [           main] o.m.e.c.g.dao.ClinVarWhiteListReader     : Reading ClinVar whitelist...
2024-09-27T16:26:48.207Z  INFO 1740148 --- [           main] o.m.e.c.g.dao.serialisers.MvStoreUtil    : MVMap 'clinvar' opened with 2353837 entries
2024-09-27T16:26:50.516Z  INFO 1740148 --- [           main] o.m.e.c.g.dao.ClinVarWhiteListReader     : Read 203570 ClinVar whitelist variants in 2320 ms
2024-09-27T16:26:50.558Z  INFO 1740148 --- [           main] o.m.e.a.genome.GenomeDataSourceLoader    : Loaded 203570 whitelist variants
2024-09-27T16:26:50.712Z  INFO 1740148 --- [           main] o.m.e.c.g.dao.serialisers.MvStoreUtil    : MVMap 'alleles' opened with 826441620 entries
2024-09-27T16:26:50.737Z  INFO 1740148 --- [           main] o.m.e.c.g.dao.serialisers.MvStoreUtil    : MVMap 'clinvar' opened with 2353837 entries
2024-09-27T16:26:51.318Z  INFO 1740148 --- [           main] g.GenomeAnalysisServiceAutoConfiguration : Configured hg19 genome analysis service
2024-09-27T16:26:52.360Z ERROR 1740148 --- [           main] com.zaxxer.hikari.pool.HikariPool        : 2402_phenotype - Exception during pool initialization.

Shall I open another thread?

Thanks again!

[lt11]

Oh, my fault in this case… let me double check it…

[julesjacobsen]

Did you add the 2402_phenotype data to that directory as well? You'll need it...

[lt11]

Indeed, my fault. I had forgotten the 2402_phenotype data. The test was succesful. Thanks a lot!