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NF-Core ampliseq - Rscript markdown error

Hello

I'm trying to get nf-core/ampliseq running on Win11 with wsl. The pipeline starts normally and does multiqc step, but then stops with an error. The same error pops up in both Singularity and Docker.

ERROR-[nf-core/ampliseq] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_AMPLISEQ:AMPLISEQ:SUMMARY_REPORT (1)'

Caused by:

 Process `NFCORE_AMPLISEQ:AMPLISEQ:SUMMARY_REPORT (1)` terminated with an error exit status (1)

Command executed:

#!/usr/bin/env Rscript
  library(rmarkdown)

Any ideas what is causing this, and how i can fix it?

nf-core ampliseq
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updated by Michael Dondrup Michael Dondrup • written by nermze • nermze

Could you try to run R in WSL and load the rmarkdown library and see what happens?
or run echo "library(rmarkdown)" | Rscript -

You might get:

$ echo "library(rmarkdown)" | Rscript -
Error in library(rmarkdown) : there is no package called ‘rmarkdown’
Execution halted

Then also try the same in singularity/docker when running in shell mode (e.g. singularity shell ... instead of singularity run). Possibly the creators of the image or work-flow forgot to install the R-package during build script or via conda. If you know where the source of the NF script is located, you can modify it.

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written by Michael Dondrup Michael Dondrup

Hi and thank you for the reply.

I have run the code as you suggested, no errors in the output. The same error with rmarkdown appears irregardless of docker or singularity.

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written by nermze • nermze

Can you provide the exact invocation for running the workflow in singularity, please?

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written by Michael Dondrup Michael Dondrup

This is the code i run;

sudo nextflow run nf-core/ampliseq -r 2.7.1 -profile singularity --iontorrent --input "16S_DATA/samples.tsv" --FW_primer GTGYCAGCMGCCGCGGTAA --RV_primer GGACTACNVGGGTWTCTAAT --outdir results/
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written by nermze • nermze

Do you need to run it as sudo ? That's generally extremely bad practice which could destroy your system :-)

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written by colindaven colindaven

In addition, this might also be the reason for the error. Even if you are working under WSL, never run user processes as a privileged user.

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written by Michael Dondrup Michael Dondrup

Could you post the .nextflow.log as well as the output of lsmem? It could be a memory problem, since WSL might not be able to access the whole memory.

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written by barslmn • barslmn

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