nextflow run nf-core/demo -r 1.0.1 -profile test,docker --outdir ./out                                                                                                          venv:base

 N E X T F L O W   ~  version 25.04.2

Launching `https://github.com/nf-core/demo` [peaceful_davinci] DSL2 - revision: 04060b4644 [1.0.1]


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  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
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  nf-core/demo 1.0.1
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Input/output options
  input                     : https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv
  outdir                    : ./out

Institutional config options
  config_profile_name       : Test profile
  config_profile_description: Minimal test dataset to check pipeline function

Core Nextflow options
  revision                  : 1.0.1
  runName                   : peaceful_davinci
  containerEngine           : docker
  launchDir                 : /Users/josuacarl/Codespace/test/test_dir
  workDir                   : /Users/josuacarl/Codespace/test/test_dir/work
  projectDir                : /Users/josuacarl/.nextflow/assets/nf-core/demo
  userName                  : josuacarl
  profile                   : test,docker
  configFiles               : /Users/josuacarl/.nextflow/config, /Users/josuacarl/.nextflow/assets/nf-core/demo/nextflow.config, /Users/josuacarl/Codespace/test/test_dir/nextflow.config

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------* The pipeline
  https://doi.org/10.5281/zenodo.12192442

* The nf-core framework
    https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
    https://github.com/nf-core/demo/blob/master/CITATIONS.md

executor >  local (2)
[de/e2425e] process > NFCORE_DEMO:DEMO:FASTQC (SAMPLE2_PE)     [  0%] 0 of 3
[3e/2aec88] process > NFCORE_DEMO:DEMO:SEQTK_TRIM (SAMPLE2_PE) [  0%] 0 of 3
[-        ] process > NFCORE_DEMO:DEMO:MULTIQC                 -
WARN: Directive `process.shell` cannot contain new-line characters - offending value: [bash

set -e # Exit if a tool returns a non-zero status/exit code
set -u # Treat unset variables and parameters as an error
set -o pipefail # Returns the status of the last command to exit with a non-zero status or zero if all successfully execute
set -C # No clobber - prevent output redirection from overwriting files.
]
ERROR ~ Error executing process > 'NFCORE_DEMO:DEMO:SEQTK_TRIM (SAMPLE2_PE)'

Caused by:
  Process `NFCORE_DEMO:DEMO:SEQTK_TRIM (SAMPLE2_PE)` terminated with an error exit status (126)


Command executed:

  printf "%s\n" sample2_R1.fastq.gz sample2_R2.fastq.gz | while read f;
  do
executor >  local (2)
[de/e2425e] process > NFCORE_DEMO:DEMO:FASTQC (SAMPLE2_PE)     [  0%] 0 of 3
[3e/2aec88] process > NFCORE_DEMO:DEMO:SEQTK_TRIM (SAMPLE2_PE) [  0%] 0 of 3
[-        ] process > NFCORE_DEMO:DEMO:MULTIQC                 -
Execution cancelled -- Finishing pending tasks before exit
WARN: Directive `process.shell` cannot contain new-line characters - offending value: [bash

set -e # Exit if a tool returns a non-zero status/exit code
set -u # Treat unset variables and parameters as an error
set -o pipefail # Returns the status of the last command to exit with a non-zero status or zero if all successfully execute
set -C # No clobber - prevent output redirection from overwriting files.
]
ERROR ~ Error executing process > 'NFCORE_DEMO:DEMO:SEQTK_TRIM (SAMPLE2_PE)'

Caused by:
  Process `NFCORE_DEMO:DEMO:SEQTK_TRIM (SAMPLE2_PE)` terminated with an error exit status (126)


Command executed:

  printf "%s\n" sample2_R1.fastq.gz sample2_R2.fastq.gz | while read f;
  do
      seqtk \
          trimfq \
           \
executor >  local (2)
[de/e2425e] process > NFCORE_DEMO:DEMO:FASTQC (SAMPLE2_PE)     [  0%] 0 of 3
[3e/2aec88] process > NFCORE_DEMO:DEMO:SEQTK_TRIM (SAMPLE2_PE) [  0%] 0 of 3
[-        ] process > NFCORE_DEMO:DEMO:MULTIQC                 -
Execution cancelled -- Finishing pending tasks before exit
-[nf-core/demo] Pipeline completed with errors-
WARN: Directive `process.shell` cannot contain new-line characters - offending value: [bash

set -e # Exit if a tool returns a non-zero status/exit code
set -u # Treat unset variables and parameters as an error
set -o pipefail # Returns the status of the last command to exit with a non-zero status or zero if all successfully execute
set -C # No clobber - prevent output redirection from overwriting files.
]
ERROR ~ Error executing process > 'NFCORE_DEMO:DEMO:SEQTK_TRIM (SAMPLE2_PE)'

Caused by:
  Process `NFCORE_DEMO:DEMO:SEQTK_TRIM (SAMPLE2_PE)` terminated with an error exit status (126)


Command executed:

  printf "%s\n" sample2_R1.fastq.gz sample2_R2.fastq.gz | while read f;
  do
      seqtk \
          trimfq \
           \
executor >  local (2)
[de/e2425e] process > NFCORE_DEMO:DEMO:FASTQC (SAMPLE2_PE)     [  0%] 0 of 3
[3e/2aec88] process > NFCORE_DEMO:DEMO:SEQTK_TRIM (SAMPLE2_PE) [  0%] 0 of 3
[-        ] process > NFCORE_DEMO:DEMO:MULTIQC                 -
Execution cancelled -- Finishing pending tasks before exit
-[nf-core/demo] Pipeline completed with errors-
WARN: Directive `process.shell` cannot contain new-line characters - offending value: [bash

set -e # Exit if a tool returns a non-zero status/exit code
set -u # Treat unset variables and parameters as an error
set -o pipefail # Returns the status of the last command to exit with a non-zero status or zero if all successfully execute
set -C # No clobber - prevent output redirection from overwriting files.
]
ERROR ~ Error executing process > 'NFCORE_DEMO:DEMO:SEQTK_TRIM (SAMPLE2_PE)'

Caused by:
  Process `NFCORE_DEMO:DEMO:SEQTK_TRIM (SAMPLE2_PE)` terminated with an error exit status (126)


Command executed:

  printf "%s\n" sample2_R1.fastq.gz sample2_R2.fastq.gz | while read f;
  do
      seqtk \
          trimfq \
           \
          $f \
          | gzip --no-name > SAMPLE2_PE_$(basename $f)
  done

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_DEMO:DEMO:SEQTK_TRIM":
      seqtk: $(echo $(seqtk 2>&1) | sed 's/^.*Version: //; s/ .*$//')
  END_VERSIONS

Command exit status:
  126

Command output:
  (empty)

Command error:
  /bin/bash: .command.run: /bin/bash: bad interpreter: Permission denied

Work dir:
  /Users/josuacarl/Codespace/test/test_dir/work/3e/2aec88e07499391d42c9dfafd975f6

Container:
  quay.io/biocontainers/seqtk:1.4--he4a0461_1

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

 -- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

 -- Check '.nextflow.log' file for details
WARN: The nf-co2footprint plugin generated the following warnings during the execution of the workflow:
	- The CPU model could not be detected for at least one task. Using default CPU power draw value!
	- The reported CPU usage is null for at least one task. Assuming 100% usage for each requested CPU!