Closed DSRYU closed 5 years ago
I remember experiencing an error like this..
After cloning Exomiser have you installed it?
mvn clean install package
from inside the cloned repo?
I tried it but it gives error. root@ubuntu:/data/reference_data/Exomiser# ls -al ~/.m2/ total 12 drwxr-xr-x 2 root root 4096 11월 22 18:29 . drwxr-xr-x 18 sysadm sysadm 4096 11월 22 18:31 .. -rw-r--r-- 1 root root 86 11월 22 18:29 settings.xml setting.xml < settings>
root@ubuntu:/data/reference_data/Exomiser# ls -al total 228 drwxr-xr-x 15 root root 4096 11월 22 18:31 . drwxr-xr-x 3 root root 4096 11월 22 18:28 .. drwxr-xr-x 2 root root 4096 11월 22 18:28 .circleci drwxr-xr-x 8 root root 4096 11월 22 18:28 .git -rw-r--r-- 1 root root 447 11월 22 18:28 .gitattributes -rw-r--r-- 1 root root 841 11월 22 18:28 .gitignore drwxr-xr-x 3 root root 4096 11월 22 18:28 .mvn -rw-r--r-- 1 root root 34519 11월 22 18:28 LICENCE -rw-r--r-- 1 root root 83957 11월 22 18:28 LOGO_IRDIRCRR_RVB.jpg -rw-r--r-- 1 root root 9366 11월 22 18:28 README.md drwxr-xr-x 2 root root 4096 11월 22 18:28 docs drwxr-xr-x 4 root root 4096 11월 22 18:28 exomiser-cli drwxr-xr-x 5 root root 4096 11월 22 18:31 exomiser-core drwxr-xr-x 4 root root 4096 11월 22 18:28 exomiser-data-genome drwxr-xr-x 4 root root 4096 11월 22 18:28 exomiser-data-phenotype drwxr-xr-x 4 root root 4096 11월 22 18:28 exomiser-rest-prioritiser drwxr-xr-x 4 root root 4096 11월 22 18:28 exomiser-spring-boot-autoconfigure drwxr-xr-x 4 root root 4096 11월 22 18:28 exomiser-spring-boot-starter drwxr-xr-x 4 root root 4096 11월 22 18:28 exomiser-spring-boot-test drwxr-xr-x 4 root root 4096 11월 22 18:28 exomiser-web -rw-r--r-- 1 root root 6468 11월 22 18:28 mvnw -rw-r--r-- 1 root root 4994 11월 22 18:28 mvnw.cmd -rw-r--r-- 1 root root 11680 11월 22 18:28 pom.xml
root@ubuntu:/data/reference_data/Exomiser# mvn clean install package [INFO] Results: [INFO] [INFO] Tests run: 0, Failures: 0, Errors: 0, Skipped: 0 [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary: [INFO] [INFO] exomiser ........................................... SUCCESS [ 0.570 s] [INFO] exomiser-core ...................................... FAILURE [ 9.206 s] [INFO] exomiser-spring-boot-autoconfigure ................. SKIPPED [INFO] exomiser-spring-boot-starter ....................... SKIPPED [INFO] exomiser-spring-boot-test .......................... SKIPPED [INFO] exomiser-cli ....................................... SKIPPED [INFO] exomiser-data-genome ............................... SKIPPED [INFO] exomiser-data-phenotype ............................ SKIPPED [INFO] exomiser-rest-prioritiser .......................... SKIPPED [INFO] exomiser-web ....................................... SKIPPED [INFO] ------------------------------------------------------------------------ [INFO] BUILD FAILURE [INFO] ------------------------------------------------------------------------ [INFO] Total time: 10.598 s [INFO] Finished at: 2018-11-22T18:37:50+09:00 [INFO] Final Memory: 52M/656M [INFO] ------------------------------------------------------------------------ [ERROR] Failed to execute goal org.apache.maven.plugins:maven-surefire-plugin:2.22.0:test (default-test) on project exomiser-core: There are test failures. [ERROR] [ERROR] Please refer to /data/reference_data/Exomiser/exomiser-core/target/surefire-reports for the individual test results. [ERROR] Please refer to dump files (if any exist) [date]-jvmRun[N].dump, [date].dumpstream and [date]-jvmRun[N].dumpstream. [ERROR] ExecutionException The forked VM terminated without properly saying goodbye. VM crash or System.exit called? [ERROR] Command was /bin/sh -c cd /data/reference_data/Exomiser/exomiser-core && /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/java '-javaagent:/root/.m2/repository/org/jacoco/org.jacoco.agent/0.8.1/org.jacoco.agent-0.8.1-runtime.jar=destfile=/data/reference_data/Exomiser/exomiser-core/target/jacoco.exec,excludes=/resources/:/assemble/' -jar /data/reference_data/Exomiser/exomiser-core/target/surefire/surefirebooter3160720047109604265.jar /data/reference_data/Exomiser/exomiser-core/target/surefire 2018-11-22T18-37-49_419-jvmRun1 surefire4075254641124906505tmp surefire_05707736014213914957tmp [ERROR] Error occurred in starting fork, check output in log .... [ERROR] Caused by: org.apache.maven.surefire.booter.SurefireBooterForkException: The forked VM terminated without properly saying goodbye. VM crash or System.exit called? [ERROR] Command was /bin/sh -c cd /data/reference_data/Exomiser/exomiser-core && /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/java '-javaagent:/root/.m2/repository/org/jacoco/org.jacoco.agent/0.8.1/org.jacoco.agent-0.8.1-runtime.jar=destfile=/data/reference_data/Exomiser/exomiser-core/target/jacoco.exec,excludes=/resources/:/assemble/' -jar /data/reference_data/Exomiser/exomiser-core/target/surefire/surefirebooter2589335864457829238.jar /data/reference_data/Exomiser/exomiser-core/target/surefire 2018-11-22T18-31-52_099-jvmRun2 surefire607711632266005679tmp surefire_26777377948123787022tmp [ERROR] Error occurred in starting fork, check output in log [ERROR] Process Exit Code: 1 [ERROR] at org.apache.maven.plugin.surefire.booterclient.ForkStarter.fork(ForkStarter.java:671) [ERROR] at org.apache.maven.plugin.surefire.booterclient.ForkStarter.fork(ForkStarter.java:533) [ERROR] at org.apache.maven.plugin.surefire.booterclient.ForkStarter.access$600(ForkStarter.java:115) [ERROR] at org.apache.maven.plugin.surefire.booterclient.ForkStarter$1.call(ForkStarter.java:362) [ERROR] at org.apache.maven.plugin.surefire.booterclient.ForkStarter$1.call(ForkStarter.java:342) [ERROR] at java.util.concurrent.FutureTask.run(FutureTask.java:266) [ERROR] at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) [ERROR] at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) [ERROR] at java.lang.Thread.run(Thread.java:748) [ERROR] -> [Help 1] [ERROR] [ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch. [ERROR] Re-run Maven using the -X switch to enable full debug logging. [ERROR] [ERROR] For more information about the errors and possible solutions, please read the following articles: [ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException [ERROR] [ERROR] After correcting the problems, you can resume the build with the command [ERROR]
Hi again. Under the ~/.m2/ folder I have these settings:
<settings>
<localRepository>${user.home}/.m3/repository</localRepository>
</settings>
Maybe this helps?
You're running whatever maven version is installed on your system. This can cause problems, so Exomiser has a bundled maven binary to prevent these issues. Run it like this:
./mvnw clean install -DskipTests=true -Dmaven.javadoc.skip=true -B -V
Thank northwestwitch for kind reply.
Dear julesjacobsen.
You're right. -DskipTests enable to compile Exomiser.
Thanks again ^^.
INFO] Reactor Summary: [INFO] [INFO] exomiser ........................................... SUCCESS [ 3.849 s] [INFO] exomiser-core ...................................... SUCCESS [ 11.169 s] [INFO] exomiser-spring-boot-autoconfigure ................. SUCCESS [ 39.635 s] [INFO] exomiser-spring-boot-starter ....................... SUCCESS [ 0.032 s] [INFO] exomiser-spring-boot-test .......................... SUCCESS [ 0.149 s] [INFO] exomiser-cli ....................................... SUCCESS [ 42.698 s] [INFO] exomiser-data-genome ............................... SUCCESS [ 43.924 s] [INFO] exomiser-data-phenotype ............................ SUCCESS [ 4.553 s] [INFO] exomiser-rest-prioritiser .......................... SUCCESS [ 45.370 s] [INFO] exomiser-web ....................................... SUCCESS [ 19.012 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------
Thanks to julesjacobsen, the Exomiser has been successfully compiled. But I have another error in compiling matchbox with mvn.
I edited pom.xml and GenotypeSimilarityServiceImplTest.java as recommended: The added infromation in pom.xml is like this(In the case of 1.9.5 version, I tried both cases, commetend or uncommented):
<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-all</artifactId>
<version>2.0.2-beta</version>
</dependency>
But matchbox maven could not recognize GenotypeSimilarityServiceImplTest class. The edited GenotypeSimilarityServiceImplTest.java is like this: //assertThat(commonGenes, equalTo(expected)); DecimalFormat df = new DecimalFormat("0.##"); assertThat(df.format(genotypeSimilarityScore.getScore()), equalTo("0.94"));
before editing GenotypeSimilarityServiceImplTest.java, it gives below error:
[INFO] --- maven-surefire-plugin:2.18.1:test (default-test) @ matchbox --- [INFO] Surefire report directory: /home/sysadm/matchbox/target/surefire-reports
오류: 기본 클래스 org.apache.maven.surefire.booter.ForkedBooter을(를) 찾거나 로드할 수 없습니다. ==> This means "Error: basic class, org.apache.maven.surefire.booter.ForkedBooter is not founded or loaded. Results :
Tests run: 0, Failures: 0, Errors: 0, Skipped: 0
[INFO] ------------------------------------------------------------------------ [INFO] BUILD FAILURE [INFO] ------------------------------------------------------------------------ [INFO] Total time: 3.277 s [INFO] Finished at: 2018-11-23T13:41:36+09:00 [INFO] Final Memory: 37M/284M [INFO] ------------------------------------------------------------------------ [ERROR] Failed to execute goal org.apache.maven.plugins:maven-surefire-plugin:2.18.1:test (default-test) on project matchbox: Execution default-test of goal org.apache.maven.plugins:maven-surefire-plugin:2.18.1:test failed: The forked VM terminated without properly saying goodbye. VM crash or System.exit called? [ERROR] Command was /bin/sh -c cd /home/sysadm/matchbox && /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/java -jar /home/sysadm/matchbox/target/surefire/surefirebooter6380962758114387402.jar /home/sysadm/matchbox/target/surefire/surefire5390621855385802781tmp /home/sysadm/matchbox/target/surefire/surefire_06289007752142453377tmp [ERROR] -> [Help 1] [ERROR]
Could you look at this more?
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.1:testCompile (default-testCompile) on project matchbox: Compilation failure [ERROR] /home/sysadm/matchbox/src/test/java/org/broadinstitute/macarthurlab/matchbox/match/GenotypeSimilarityServiceImplTest.java:[173,30] cannot find symbol [ERROR] symbol: variable genotypeSimilarityScore [ERROR] location: class org.broadinstitute.macarthurlab.matchbox.match.GenotypeSimilarityServiceImplTest [ERROR] -> [Help 1]
About the failing test, It's due to a bug that I described in another issue (#54) and has to be fixed before having a full functioning version of the software. But if you want to install Matchbox to test it you should modify this test first, otherwise it doesn't install.
Thanks northwestiwitch.
About the matchbox compile, it has been successfully compiled without test process. When I run the compiled matchbox with below command, it gave other errors like belows: root@ubuntu:~/matchbox# java -jar target/matchbox-0.1.0.jar --server.port=9020 I think it would be caused by converting modules gene symbols to ensembl id. How can I solve it? Best regards, 2018-11-26 16:24:25.446 INFO 12055 --- [ main] o.m.e.a.DataDirectoryAutoConfiguration : Exomiser data directory set to: /data/reference_data/Exomiser 2018-11-26 16:24:25.471 INFO 12055 --- [ main] com.zaxxer.hikari.HikariDataSource : exomiser-phenotype-1807 - Started. 2018-11-26 16:24:25.919 ERROR 12055 --- [ main] o.b.m.matchbox.metrics.BaseMetric : Error reading gene symbol to emsembl id map:java.lang.NullPointerException : null
.... 2018-11-26 16:24:26.441 INFO 12055 --- [ main] org.mongodb.driver.connection : Opened connection [connectionId{localValue:2, serverValue:26}] to 147.47.106.196:27017 2018-11-26 16:24:26.493 ERROR 12055 --- [ main] o.b.m.matchbox.metrics.BaseMetric : Error reading gene symbol to emsembl id map:java.lang.NullPointerException : null 2018-11-26 16:24:26.496 ERROR 12055 --- [ main] o.b.m.matchbox.metrics.BaseMetric : Error reading gene symbol to emsembl id map:java.lang.NullPointerException : null 2018-11-26 16:24:26.511 INFO 12055 --- [ main] o.b.m.m.config.MatchMakerNodeConfig : Reading MME nodes from /home/sysadm/matchbox/config/nodes.json
Hi, I see the same error when I launch the server. I don't know what the cause!
Hello,
I am trying to install using maven. This version also gives the error as below messages:
[ERROR] Failed to execute goal on project matchbox: Could not resolve dependencies for project org.broadinstitute.macarthurlab:matchbox:jar:0.1.0: The following artifacts could not be resolved: org.monarchinitiative.exomiser:exomiser-spring-boot-starter:jar:11.0.0, org.monarchinitiative.exomiser:exomiser-spring-boot-test:jar:11.0.0: Could not find artifact org.monarchinitiative.exomiser:exomiser-spring-boot-starter:jar:11.0.0 in central (https://repo.maven.apache.org/maven2) -> [Help 1] [ERROR] [ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch. [ERROR] Re-run Maven using the -X switch to enable full debug logging. [ERROR] [ERROR] For more information about the errors and possible solutions, please read the following articles: [ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/DependencyResolutionException
The version of maven is Apache Maven 3.3.9 . root@ubuntu:~/.m2/matchbox# mvn -version Apache Maven 3.3.9 Maven home: /usr/share/maven Java version: 1.8.0_181, vendor: Oracle Corporation Java home: /usr/lib/jvm/java-8-openjdk-amd64/jre Default locale: ko_KR, platform encoding: UTF-8 OS name: "linux", version: "4.4.0-96-generic", arch: "amd64", family: "unix"
The Exomiser directory structure is as follows: root@ubuntu:~/.m2# tree -L 1 Exomiser Exomiser ├── 1807_phenotype ├── 1807_phenotype.tar.gz ├── LICENCE ├── LOGO_IRDIRCRR_RVB.jpg ├── README.md ├── docs ├── exomiser-cli ├── exomiser-core ├── exomiser-data-genome ├── exomiser-data-phenotype ├── exomiser-rest-prioritiser ├── exomiser-spring-boot-autoconfigure ├── exomiser-spring-boot-starter ├── exomiser-spring-boot-test ├── exomiser-web ├── mvnw ├── mvnw.cmd └── pom.xml
I also edited the part of application.properties file. root@ubuntu:~/.m2# vi matchbox/src/main/resources/application.properties
matchbox.gene-symbol-to-id-mappings=${user.dir}/config/gene_symbol_to_ensembl_id_map.txt matchbox.connected-nodes=${user.dir}/config/nodes.json exomiser.data-directory=/home/sysadm/.m2/Exomiser exomiser.phenotype.data-version=1807
I used below command for installation. root@ubuntu:~/.m2/matchbox# mvn clean install package
Could you help me?