Error at phase 4 when running GeMoMa (homology-based annotation)

Question

[bbscience]

I am using two external GFF's of related organisms to perform a homology annotation approach for a de novo genome assembly. This is my code and the error output I received at stage 4 - error with the 'GeMoMa Annotation Filter' so that no final GFF file was produced. Please let me know if anyone else has received this error or if there are some solutions to this.

java -Xmx34g -jar /home//GeMoMa-1/GeMoMa-1.8.jar CLI GeMoMaPipeline threads=20 AnnotationFinalizer.r=NO p=false o=true t=/home/genome.fasta outdir=output_GeMoMa/ s=own I=genome2 a=/home/genome2.gff g=/home/genome2.fna s=own I=genome3 a=/home/genome3.gff g=/home/genome3.fna 

starting phase 4 (74005.009s)
=============================
Starting: GAF (74005.009s)
all: 260739
java.lang.NullPointerException: Cannot invoke "javax.script.ScriptEngine.createBindings()" because "engine" is null
        at projects.gemoma.Tools.eval(Tools.java:698)
        at projects.gemoma.Tools.filter(Tools.java:731)
        at projects.gemoma.GeMoMaAnnotationFilter.run(GeMoMaAnnotationFilter.java:432)
        at projects.gemoma.GeMoMaPipeline$JGAF.doJob(GeMoMaPipeline.java:2114)
        at projects.gemoma.GeMoMaPipeline$FlaggedRunnable.run(GeMoMaPipeline.java:1370)
        at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:539)
        at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
        at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:539)
        at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
        at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
        at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
        at java.base/java.lang.Thread.run(Thread.java:833)


Statistics:
Job     WAITING RUNNING INTERRUPTED     FAILED  SUCCEEDED
---------------------------------------------------------
MmseqsCreateDB  0       0       0       0       1
EREAndFill      0       0       0       0       1
ExtractorAndSplit       0       0       0       0       2
Mmseqs  0       0       0       0       2
GeMoMa  0       0       0       0       40
Cat     0       0       0       0       2
GAF     0       0       0       1       0

1 jobs did not finish as expected. Please check the output carefully.
Did not delete temporary files allowing to debug.

Elapsed time: 74009 seconds     (20h 33m 29s)
Exception in thread "main" java.lang.RuntimeException: Did not finish as intended. java.lang.NullPointerException: Cannot invoke "javax.script.ScriptEngine.createBindings()" because "engine" is null
        at projects.gemoma.Tools.eval(Tools.java:698)
        at projects.gemoma.Tools.filter(Tools.java:731)
        at projects.gemoma.GeMoMaAnnotationFilter.run(GeMoMaAnnotationFilter.java:432)
        at projects.gemoma.GeMoMaPipeline$JGAF.doJob(GeMoMaPipeline.java:2114)
        at projects.gemoma.GeMoMaPipeline$FlaggedRunnable.run(GeMoMaPipeline.java:1370)
        at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:539)
        at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
        at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:539)
        at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
        at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
        at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)

Answer 1

[asd63zhengzeyu]

You have to downgrade you java version to older than 15

https://github.com/Jstacs/Jstacs/issues/35