nanopore long sequencing DNA data data basecalling using EPI2ME ,NEXTFLOW and singualrity in cluster env have error : ERROR ~ Error executing process > 'getParams' Caused by: Process `getParams` te

Question

[reziyamaimaiti0331]

nanopore long sequencing DNA data data basecalling using EPI2ME ,NEXTFLOW and singualrity in cluster env have error : ERROR ~ Error executing process > 'getParams' Caused by: Process getParams , what is that mean?and how to solve this.

[GenoMax]

Do you know if singularity is working properly on your cluster? This is likely not the only error. There may be some other issues. You can post the entire log on a site such as pastebin.com and provide that link.

[reziyamaimaiti0331]

my version of singularity is 2.4.6-master.g55b3733,is this the problem ? what is the requirement for version ?

[dthorbur]

This sounds like an error before the processes are even launched. Could be anything from a syntax error to container error and more. Can you provide any relevant parts of the .nextflow.log?

[reziyamaimaiti0331]

executor {
    $local {
        cpus = 12
        memory = "40 GB"
    }
}


basecaller_nf_config.cfg (END)   

This is my config file ,but in the error massage i see two config file :

/home/m/.nextflow/assets/epi2me-labs/wf-basecalling/nextflow.config, /fast/A/R/dimeloseqrun/basecaller_nf_config.cfg,

[dthorbur]

This was not the file I suggested. The .nextflow.log file shows the logging for the run. It's usually hidden because of the . at the start of the file name. Regardless, the $ before local looks like a syntax error to me. Unless this is a different variable already set previously.

Did you write an additional config file? epi2me-labs provide a default one that loads the required parameters with their profiles. I don't know if loading an additional one can cause a clash. What command are you using to run the pipeline?

[colindaven]

It is having an error getting the parameters. Why not show the config file and the command you are using to run the pipeline?