Closed pnrobinson closed 4 years ago
The current Jannovar has for TranscriptModel
private static final long serialVersionUID = 4L;
I was using the very latest 1902 data version, strange--check this.
THis works on linux
simulate-vcf
-e /.../data/exomiser/1811_hg19
--phenopacket Kumada-2004-AA06-case_1-Arima.json
--template-vcf
/..../project.NIST.hc.snps.indels.NIST7035.vcf
-x
test
-m
10
This is rather odd. The only change with exomiser 12.1.0 was to add in the ID from the VCF - there were no other changes at all. Damian hasn't mentioned any issues like this - are you generating your own .ser files?
Things are working perfectly on my linux box, but I did need to add a Jannovar dependency explicitly to the LIRICAL pom file -- it seems Exomiser is no longer providing this transitively (correspondingly, the maven enforcer seems to be content). I will re-check the Mac version today, maybe there was something else going on too.
Uncertain why, but with a number of other bug fixes, this seems to be working now.
Still getting this now There is some version issue (TranscriptModel) local class incompatible: stream class desc serialVersionUID = 4, local class serialVersionUID = 3 @julesjacobsen Any idea what might be going on? This is the most recent version of LIRICAL and the 1902 Exomiser data. Apparently, it does not happen on ubuntu Command:
simulate-vcf
-e
/Users/peterrobinson/Documents/data/exomiser/1902_hg19
-p
/Users/peterrobinson/Desktop/PhenopacketsForSimulations/original/Bee-2015-BBS2-II_2.json
-v
/Users/peterrobinson/Documents/data/lirical/project.NIST.hc.snps.indels.NIST7035.vcf
-x
BBS2
Error/crash:
[ERROR] LiricalFactory - LiricalFactory.javaorg.monarchinitiative.lirical.configuration.LiricalFactory.jannovarData(LiricalFactory.java:435) - Could not deserialize Jannovar file with legacy deserializer...
Exception in thread "main" org.monarchinitiative.lirical.exception.LiricalRuntimeException: Could not load Jannovar data from /Users/peterrobinson/Documents/data/exomiser/1902_hg19/1902_hg19_transcripts_refseq.ser (Could not deserialize data list: java.io.InvalidClassException: de.charite.compbio.jannovar.reference.TranscriptModel; local class incompatible: stream classdesc serialVersionUID = 4, local class serialVersionUID = 3)
I can't reproduce this error. @pnrobinson could you send me that VCF:
project.NIST.hc.snps.indels.NIST7035.vcf
and phenopacket:
Bee-2015-BBS2-II_2.json
?
Also, have you tried this with the 1909_hg19 exomiser data?
This command runs for me using 1909_hg19 (although I do get an unrelated NullPointerException)
Thanks for the vcf/phenotpacker Peter.
I've run this thusly, and things run to completion for me on my Mac using 1909_hg19. I will see if I can reproduce this issue using 1902_hg19.
/Library/Java/JavaVirtualMachines/jdk1.8.0_131.jdk/Contents/Home/bin/java -Dfile.encoding=UTF-8 -jar /Users/jtr4v/IdeaProjects/LIRICAL/target/LIRICAL.jar simulate-vcf
-e /Users/jtr4v/IdeaProjects/LIRICAL/data/1909_hg19/
-p /Users/jtr4v/IdeaProjects/LIRICAL/example_data/peter_vcf_sim/peter_vcf_sim.json
-v /Users/jtr4v/IdeaProjects/LIRICAL/example_data/peter_vcf_sim/peter_vcf_sim.vcf -x BBS2
SLF4J: Class path contains multiple SLF4J bindings.
SLF4J: Found binding in [jar:file:/Users/jtr4v/IdeaProjects/LIRICAL/target/LIRICAL.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in [jar:file:/Users/jtr4v/IdeaProjects/LIRICAL/target/lib/log4j-slf4j-impl-2.12.0.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation.
SLF4J: Actual binding is of type [org.apache.logging.slf4j.Log4jLoggerFactory]
peter_vcf_sim.json BARDET-BIEDL SYNDROME 2; BBS2 OMIM:615981 NCBIGene:583 1 1 0.999990
1: 1 (100.0%)
1: 1 (100.0%) [by gene]
LIRICAL: Elapsed time was 1 min, 5 sec
Process finished with exit code 0
updateing to 1909 seems to ave solved the issue.
On Mac, IntelliJ no longer recognizes the Jannovar imports (which were supposed to be coming transitively from Exomiser, but may not be with the upgrade to 12.1.0 @julesjacobsen thoughts?)
The key is an issue with the class TranscriptModel: