Unexpected error [InvocationTargetException]

[yang-guoli]

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

and I am a newbie in bioinformatics，could you help me?

[drpatelh]

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]

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]

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

[Argonvi]

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:

[Argonvi]

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.