resolve error 255 or Rscript execution error: No such file or directory

[Theo]

Hi all,
For some unknown reason my nextflow stopped working:

the command is the following:

./nextflow -C rnadepipe/nextflow_local_tgeorgom.config run rnadepipe/main_tgeorgom.nf --config rnadepipe/data/JHA04_new.json -resume cheesy_heyrovsky

and all went well till:

N E X T F L O W  ~  version 20.07.1
Launching `rnadepipe/main_tgeorgom.nf` [prickly_montalcini] - revision: 15d13597de
executor >  local (1), slurm (1)
executor >  local (1), slurm (1)
[13/ef9aac] process > renameRawFastq (Cntrl143)      [100%] 13 of 13, cached: 13 ✔
[13/820393] process > fastqc_raw (KL92)              [100%] 13 of 13, cached: 13 ✔
[e7/f10723] process > trimmomatic (LMNA_381II)       [100%] 13 of 13, cached: 13 ✔
[5a/bf08d0] process > fastqc_trimmed (A656)          [100%] 13 of 13, cached: 13 ✔
[skipped  ] process > STARbuildIndex                 [100%] 1 of 1, stored: 1 ✔
[40/dd0a82] process > STARalign (LMNA_331I)          [100%] 13 of 13, cached: 13 ✔
[97/1b4e00] process > generateSampleTable            [100%] 1 of 1, cached: 1 ✔
[fd/e11b3e] process > featureCounts                  [100%] 1 of 1, cached: 1 ✔
[-        ] process > multiqc                        -
[60/dff060] process > prepareDDSfromFeatureCounts    [100%] 1 of 1, failed: 1 ✘
[-        ] process > DESeq2                         -
[-        ] process > getAnnotationDb                -
[-        ] process > DEannotateResults              -
[-        ] process > enrichmentAnalysis             -
[-        ] process > writeCountsAndDEresultsToExcel -
[-        ] process > writeEnrichResultsToExcel      -
[-        ] process > interactivePlots               -
[-        ] process > publishReadme                  -
[skipping] Stored process > STARbuildIndex
value: /home/tgeorgom/work/97/1b4e0058a19ad99af7306c3b66ebf2/sampleTable.tsv
value: /home/tgeorgom/work/fd/e11b3e646df949efd2afff063ca035/geneCounts.txt
Error executing process > 'prepareDDSfromFeatureCounts'

The complete error is in here: https://pastebin.com/RMXYAzpn

going into the corresponding work directory and executing the .command.run (click for the link)  I got:

bash .command.run
nxf-scratch-dir raptor1.raptor:/scratch/nf_tmp_tgeorgom/nxf.5mPTAL3HWP
Rscript execution error: No such file or directory

The main.nf process:

if (params.QUANTIFICATION == "featureCounts") {

process prepareDDSfromFeatureCounts {

    

    label 'single_core'

    label 'fast'

    input:

    file(sampleTable) from sampleTable_ch

    sampleTable_ch.view { "value: $it" }

    file(geneCounts) from geneCounts_ch

    geneCounts_ch.view { "value: $it" }

    output:

    file("dds.RData") into dds_rdata

    script:

    """

    prepareDDSfromFeatureCounts.R

    """

    }

}

Any idea?

Thank you all
Theo

[Theo]

I forgot to mention that the directory of the rnadepipe folder consists of the subfolders "bin", "data". In bin exist all R scripts.

Thank you again.

[Philippe La Rosa]

Hi Theo,

You can use :

# cd rnadepipe/

# ../nextflow -C nextflow_local_tgeorgom.config run main_tgeorgom.nf --config data/JHA04_new.json -resume 

Philippe

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[Theo]

Hi Philippe,
Thank you for your answer.

What I am trying to do is find out what I might have changed in my environment to ending up with an unused process. There were some updates and things changed, but I do not know what.

So, the question might have been: where should I look to change back to the original settings. I have a dozen of R script in the bin folder and the nextflow program was always outside the rnadepipe folder. Somehow I have managed to have the enviroments in order.

Hope the above make sense

Best

Theo

[Theo]

Just to add that I rerun the whole pipeline and failed at the first process that uses R scripts from the rnadepipe/bin folder. I am at lost on how I managed to let nextflow knows where the R scripts ar.

[Dan]

Hi Theo,

Your nextflow is having trouble finding your R script. If the R script is in rnadepipe/bin/ as you mentioned, try:

script:

    """

    ${workflow.projectDir}/bin/prepareDDSfromFeatureCounts.R

    """

${workflow.projectDir} is where the main nextflow script (for you, main_tgeorgom.nf) locates. Without explicit specification of the folder path with ${workflow.projectDir}, you'll have to make sure the R script is in the right folder that nextflow searches for, which can be tricky sometimes.

Dan

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[Theo]

Dear all,

I noticed that there were some updates on our servers.

That resulted in the bad resolution of symlinks etc. As soon as I reset the enviroment the pipeline worked again!

Weird, because I have at this point have no idea how this works.

Best

Theo