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phelelani / nf-rnaSeqMetagen

Metagenomics pipeline
MIT License
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Command 'ps' required by nextflow to collect task metrics cannot be found #4

Open Rohit-Satyam opened 2 years ago

Rohit-Satyam commented 2 years ago

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
Rohit-Satyam commented 2 years ago

I tried running this pipeline on cluster and I get a new error

nextflow run nf-rnaSeqMetagen -profile slrum--data combined/ --genome $PWD/hg38_gencode/GRCh38.primary_assembly.genome.fa --genes $PWD/hg38_gencode/gencode.v40.primary_assembly.annotation.gtf --db $PWD/pluspf/ --mode run.FilterClassify -resume

I desperately need your help here: 

Execution command   : nextflow run nf-rnaSeqMetagen -profile slurm --data combined/ --genome /ibex/scratch/satyamr/KR_project/hg38_gencode/GRCh38.primary_assembly.genome.fa --genes /ibex/scratch/satyamr/KR_project/hg38_gencode/gencode.v40.primary_assembly.annotation.gtf --db /ibex/scratch/satyamr/KR_project/pluspf/ --mode run.FilterClassify -resume
Execution name      : disturbed_turing
Workflow start      : 2022-11-05T00:53:30.301672+03:00
[93/777c32] process > run_STAR (M-21-5392)    [  0%] 1 of 115, failed: 1
[-        ] process > run_FixSeqNames         -
[-        ] process > run_KrakenClassifyReads -
[-        ] process > run_TrinityAssemble     -
[-        ] process > run_KrakenClassifyFasta -
[-        ] process > run_KronaReport         -
[-        ] process > run_CollectTaxSeqs      -
[-        ] process > run_MultiQC             -
[-        ] process > run_CopyUpsetDir        [  0%] 0 of 1
[-        ] process > run_PrepareMatrixData   -
[-        ] process > run_CreateMatrix        -
Oohhh DANG IT!!... Pipeline execution stopped with the following message: null
Error executing process > 'run_STAR (M-21-5392)'

Caused by:
  Not a valid config attribute: executor.retry.delay -- Missing element: executor

Command executed:

  sbatch .command.run

Command exit status:
  -

Command output:
  (empty)

Work dir:
  /ibex/scratch/satyamr/KR_project/work/93/777c32298b4189d51f90d7ce5fe392

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

Besides, it is quite annoying to get this message every time I try resuming pipeline. How can this be turned off:

Trace file already exists: /ibex/scratch/satyamr/KR_project/results_nf-rnaSeqMetagen/workflow-tracing/nf-rnaSeqMetagen_trace.txt