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nf-core / rnaseq

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
https://nf-co.re/rnaseq
MIT License
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Unexpected error [InvocationTargetException] #516

Open yang-guoli opened 4 years ago

yang-guoli commented 4 years ago

When i use the command：./nextflow run nf-core/rnaseq -profile docker --input /home/young/miniconda3/bin/samplesheet.csv --genome GRCh37，it report the error that . The same error when i use the command: ./nextflow run nf-core/rnaseq -profile docker --input /home/young/miniconda3/bin/samplesheet.csv --fasta /home/young/miniconda3/bin/genome.fa --gtf /home/young/miniconda3/bin/genes.gtf.gz --gff /home/young/miniconda3/bin/genes.gff.gz --transcript_fasta /home/young/miniconda3/bin/transcriptome.fasta --addtional_fasta /home/young/miniconda3/bin/gfp.fa.gz star_index /home/young/miniconda3/bin/star.tar.gz --histat2_index /home/young/miniconda3/bin/hisat2.tar.gz --rsem_index /home/young/miniconda3/bin/rsem.tar.gz --salmon_index /home/young/miniconda3/bin/salmon.tar.gz I am a newbie in bioinformatics image and I am a newbie in bioinformatics，could you help me?

drpatelh commented 4 years ago

Hi @yang-guoli. Please check that all of the input files you have defined in the input samplesheet actually exist. This has come up more than once now and the issue is most likely because the pipeline can't find the input files. If all else fails you can try and move the fastq files to the directory where you are running the pipeline too to see if it works.

yang-guoli commented 4 years ago

Hi @yang-guoli. Please check that all of the input files you have defined in the input samplesheet actually exist. This has come up more than once now and the issue is most likely because the pipeline can't find the input files. If all else fails you can try and move the fastq files to the directory where you are running the pipeline too to see if it works.

Okay, thank you for your help and it helped me a lot

drpatelh commented 4 years ago

Great! I am assuming that solved the issue here so will close it.

Argonvi commented 2 months ago

I have gotten a very similar error, java.lang.reflect.InvocationTargetException, when running version 3.15.1 on a SLURM-managed cluster. I checked that all files in the samplesheet exist.

I run the pipeline from a folder with this nextflow.config file:

singularity { enabled = true autoMounts = true // Nextflow automatically mounts host paths in the executed container cacheDir = '/mnt/zonahpc/home/onco/comun/software/singularity/cache' } process { executor = 'slurm' }

Here is a screenshot of the execution report: Image

Argonvi commented 2 months ago

My error may be related to issue #1390 , as the log file indicated an error in line 606 of the quantify_pseudo_alignment main script.

... Oct-04 10:07:00.905 [Actor Thread 39] ERROR nextflow.extension.OperatorImpl - @unknown java.lang.reflect.InvocationTargetException: null 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 nextflow.script.FunctionDef.invoke_a(FunctionDef.groovy:64) at nextflow.script.ComponentDef.invoke_o(ComponentDef.groovy:40) at nextflow.script.WorkflowBinding.invokeMethod(WorkflowBinding.groovy:103) at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321) at nextflow.script.BaseScript.invokeMethod(BaseScript.groovy:155) at org.codehaus.groovy.vmplugin.v8.IndyGuardsFiltersAndSignatures.invokeGroovyObjectInvoker(IndyGuardsFiltersAndSignatures.java:151) at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321) at Script_3133588d453f68ad.getInferexperimentStrandedness(Script_3133588d453f68ad:606) ...

Modifying the stranded threshold to 0.7 and unstranded threshold to 0.2 allowed the pipeline to run to completion.