Hello, I have been trying to test different Kmer sizes for the assembly of long reads using NGSEP Assembler, but when I try to execute sizes other than 15, it generates the following error:
Exception in thread "main" java.lang.reflect.InvocationTargetException
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at ngsep.NGSEPcore.main(NGSEPcore.java:66)
Caused by: JSci.maths.statistics.OutOfRangeException: The variance should be (strictly) positive.
at JSci.maths.statistics.NormalDistribution.<init>(Unknown Source)
at ngsep.assembly.AssemblyGraph.predictRepetitiveVertices(AssemblyGraph.java:827)
at ngsep.assembly.AssemblyGraph.updateScores(AssemblyGraph.java:974)
at ngsep.assembly.Assembler.run(Assembler.java:485)
at ngsep.assembly.Assembler.run(Assembler.java:289)
at ngsep.assembly.Assembler.main(Assembler.java:282)
... 5 more</init>
Could you help me solve it?
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Thanks for your interest in NGSEP. Looking at the code, it seems like the software is getting trouble to identify edges. Please share the log of the process and perhaps some information on the number of reads, technology and expected genome size, to track the error.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Great, I checked the log and the problem is that you set a kmer length of 45bp and the current implementation only can take kmer lengths up to 31 bp. Unfortunatey, because of the threading, it keeps trying to process reads and at the end it fails because it finds zero edges. A k-mer length of 31 should be more than enough to assemble bacterial samples.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Hello, I have been trying to test different Kmer sizes for the assembly of long reads using NGSEP Assembler, but when I try to execute sizes other than 15, it generates the following error:
Exception in thread "main" java.lang.reflect.InvocationTargetException
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at ngsep.NGSEPcore.main(NGSEPcore.java:66)
Caused by: JSci.maths.statistics.OutOfRangeException: The variance should be (strictly) positive.
at JSci.maths.statistics.NormalDistribution.<init>(Unknown Source)
at ngsep.assembly.AssemblyGraph.predictRepetitiveVertices(AssemblyGraph.java:827)
at ngsep.assembly.AssemblyGraph.updateScores(AssemblyGraph.java:974)
at ngsep.assembly.Assembler.run(Assembler.java:485)
at ngsep.assembly.Assembler.run(Assembler.java:289)
at ngsep.assembly.Assembler.main(Assembler.java:282)
... 5 more</init>
Could you help me solve it?
Hi Diego
Thanks for your interest in NGSEP. Looking at the code, it seems like the software is getting trouble to identify edges. Please share the log of the process and perhaps some information on the number of reads, technology and expected genome size, to track the error.
I am conducting tests with different datasets, and this particular one corresponds to Escherichia coli (4.5 Mb) with 47,910 PacBio reads.
https://drive.google.com/file/d/1ZQPnF4_gD51R3VCfhhBIZP1tMCuFiTNU/view?usp=sharing
I tried to attach the file directly, but it didn't work, so I'll provide a link to Google Drive instead.
Hi Diego
Great, I checked the log and the problem is that you set a kmer length of 45bp and the current implementation only can take kmer lengths up to 31 bp. Unfortunatey, because of the threading, it keeps trying to process reads and at the end it fails because it finds zero edges. A k-mer length of 31 should be more than enough to assemble bacterial samples.