phelelani / nf-rnaseqmetagen

Metagenomics pipeline

nf-rnaSeqMetagen

biotools:nf-rnaseqmetagen

nf-rnaSeqMetagen is a Nextflow

For detailed documentation: https://phelelani.github.io/nf-rnaSeqMetagen/

nf-rnaseqmetagen's Issues

Command 'ps' required by nextflow to collect task metrics cannot be found

Hi, I am getting the following error while running this pipeline:

nextflow run nf-rnaSeqMetagen -profile standard --mode run.FilterClassify --data ~/Documents/KR_Project/combined/ --genome ~/Documents/references/hg38_gencode/GRCh38.primary_assembly.genome.fa --genes ~/Documents/references/hg38_gencode/gencode.v40.primary_assembly.annotation.gtf --db ~/Documents/Dr_Turki_Data/resources/pluspf/ --max_cpus 10

Workflow start      : 2022-11-03T02:59:58.115093063+03:00
executor >  local (5)
[59/66337e] process > run_STAR (M-21-5435)               [  0%] 0 of 121
[-        ] process > run_FixSeqNames                    -
[-        ] process > run_KrakenClassifyReads            -
[-        ] process > run_TrinityAssemble                -
[-        ] process > run_KrakenClassifyFasta            -
[-        ] process > run_KronaReport                    -
[-        ] process > run_CollectTaxSeqs                 -
[-        ] process > run_MultiQC                        -
[b4/f61ed0] process > run_CopyUpsetDir (Copy UpSet Tool) [100%] 1 of 1, failed: 1 ✘
[-        ] process > run_PrepareMatrixData              -
[-        ] process > run_CreateMatrix                   -
Oohhh DANG IT!!... Pipeline execution stopped with the following message: Command 'ps' required by nextflow to collect task metrics cannot be found
Error executing process > 'run_CopyUpsetDir (Copy UpSet Tool)'

Caused by:
  Process `run_CopyUpsetDir (Copy UpSet Tool)` terminated with an error exit status (1)

Command executed:

  /bin/hostname
  rsync -avhP /opt/upset/* .

Command exit status:
  1

Command output:
  (empty)

Command error:
  Command 'ps' required by nextflow to collect task metrics cannot be found

Work dir:
  /home/subudhak/Documents/KR_Project/rnaseqmetagen/work/b4/f61ed05a00138db7517ad0821b5eb2

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

DSL2 compatibility

Hi,

Have you tested this on DSL2?

Error when executing the main pipeline using the test data

Thanks for the wonderful tool!

I am trying to get familiar with the pipeline by using the test data you provide. However, I ran into error when I was trying to execute the main nf-rnaSeqMetagen pipeline (reference link).

After running nextflow run nf-rnaSeqMetagen -profile slurm --mode run.FilterClassify -c myparams.config, it shows error:

Unknown method invocation div on ConfigObject type

I googled around but couldn't fix it. Do you happen to know why? Thanks!

Remove scratch parameter from nextflow.config

Setting scratch with an absolute path in the pipeline nextflow.config breaks the tutorial example:

nf-rnaSeqMetagen/nextflow.config

Line 151 in 3375836

scratch = '/home/phelelani/tmp'

Should move this parameter to your personal ~/.nexflow/config