Test run for fetchngs failed

[dalinlee]

Description of the bug

Test run on the minimal dataset failed

Command used and terminal output

Command
nextflow run nf-core/fetchngs -profile test docker

Output
Core Nextflow options
  revision                  : master
  runName                   : nauseous_yalow
  launchDir                 : /home/dalin/nf_core
  workDir                   : /home/dalin/nf_core/work
  projectDir                : /home/dalin/.nextflow/assets/nf-core/fetchngs
  userName                  : dalin
  profile                   : test
  configFiles               : /home/dalin/.nextflow/assets/nf-core/fetchngs/nextflow.config

Input/output options
  input                     : https://raw.githubusercontent.com/nf-core/test-datasets/fetchngs/sra_ids_test.txt

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

Max job request options
  max_cpus                  : 2
  max_memory                : 6 GB
  max_time                  : 6h

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use nf-core/fetchngs for your analysis please cite:

* The pipeline
  https://doi.org/10.5281/zenodo.5070524

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

* Software dependencies
  https://github.com/nf-core/fetchngs/blob/master/CITATIONS.md
------------------------------------------------------
executor >  local (28)
[91/de6dcf] process > NFCORE_FETCHNGS:SRA:SRA_IDS... [ 70%] 7 of 10
[38/346b04] process > NFCORE_FETCHNGS:SRA:SRA_RUN... [100%] 7 of 7
[1b/9ccda1] process > NFCORE_FETCHNGS:SRA:SRA_FAS... [  0%] 0 of 4
[6b/3f1324] process > NFCORE_FETCHNGS:SRA:SRA_FAS... [ 62%] 5 of 8, failed: 5..
[-        ] process > NFCORE_FETCHNGS:SRA:SRA_FAS... -
[-        ] process > NFCORE_FETCHNGS:SRA:SRA_TO_... -
[-        ] process > NFCORE_FETCHNGS:SRA:SRA_MER... -
[-        ] process > NFCORE_FETCHNGS:SRA:MULTIQC... -
[-        ] process > NFCORE_FETCHNGS:SRA:CUSTOM_... -
executor >  local (30)
[91/de6dcf] process > NFCORE_FETCHNGS:SRA:SRA_IDS... [ 70%] 7 of 10
[38/346b04] process > NFCORE_FETCHNGS:SRA:SRA_RUN... [100%] 7 of 7
[1b/9ccda1] process > NFCORE_FETCHNGS:SRA:SRA_FAS... [  0%] 0 of 4
[bd/9bd173] process > NFCORE_FETCHNGS:SRA:SRA_FAS... [ 66%] 6 of 9, failed: 6..
[-        ] process > NFCORE_FETCHNGS:SRA:SRA_FAS... -
[-        ] process > NFCORE_FETCHNGS:SRA:SRA_TO_... -
[-        ] process > NFCORE_FETCHNGS:SRA:SRA_MER... -
[-        ] process > NFCORE_FETCHNGS:SRA:MULTIQC... -
[-        ] process > NFCORE_FETCHNGS:SRA:CUSTOM_... -
[68/a3b0c4] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_SRATOOLS:SRATOOLS_PREFETCH (SRR14593545)` terminated with an error exit status (1) -- Execution is retried (1)
[2d/b2d3a5] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_SRATOOLS:SRATOOLS_PREFETCH (SRR14709033)` terminated with an error exit status (1) -- Execution is retried (1)
[9a/02508e] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_SRATOOLS:SRATOOLS_PREFETCH (SRR12848126)` terminated with an error exit status (1) -- Execution is retried (1)
[29/3ce30d] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_SRATOOLS:SRATOOLS_PREFETCH (SRR14709033)` terminated with an error exit status (1) -- Execution is retried (2)
[c1/c5b350] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_SRATOOLS:SRATOOLS_PREFETCH (SRR14593545)` terminated with an error exit status (1) -- Execution is retried (2)
[b3/0c2b7d] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_SRATOOLS:SRATOOLS_PREFETCH (SRR12848126)` terminated with an error exit status (1) -- Execution is retried (2)
Error executing process > 'NFCORE_FETCHNGS:SRA:SRA_FASTQ_SRATOOLS:SRATOOLS_PREFETCH (SRR14709033)'

Caused by:
  Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_SRATOOLS:SRATOOLS_PREFETCH (SRR14709033)` terminated with an error exit status (1)

Command executed:

  eval "$(vdb-config -o n NCBI_SETTINGS | sed 's/[" ]//g')"
  if [[ ! -f "${NCBI_SETTINGS}" ]]; then
      mkdir -p "$(dirname "${NCBI_SETTINGS}")"
      printf '/LIBS/GUID = "b6aa337c-d642-4239-a4ab-552792ae78b2"\n/libs/cloud/report_instance_identity = "true"\n' > "${NCBI_SETTINGS}"
  fi

  retry_with_backoff.sh prefetch \
       \
      --progress \
      SRR14709033

  vdb-validate SRR14709033

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_FETCHNGS:SRA:SRA_FASTQ_SRATOOLS:SRATOOLS_PREFETCH":
      sratools: $(prefetch --version 2>&1 | grep -Eo '[0-9.]+')
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  .command.sh: line 2: vdb-config: command not found
  .command.sh: line 3: NCBI_SETTINGS: unbound variable

executor >  local (30)
[e7/f6dad9] process > NFCORE_FETCHNGS:SRA:SRA_IDS... [100%] 7 of 7
[38/346b04] process > NFCORE_FETCHNGS:SRA:SRA_RUN... [100%] 7 of 7
[-        ] process > NFCORE_FETCHNGS:SRA:SRA_FAS... -
[bd/9bd173] process > NFCORE_FETCHNGS:SRA:SRA_FAS... [100%] 9 of 9, failed: 9..
[-        ] process > NFCORE_FETCHNGS:SRA:SRA_FAS... -
[-        ] process > NFCORE_FETCHNGS:SRA:SRA_TO_... -
[-        ] process > NFCORE_FETCHNGS:SRA:SRA_MER... -
[-        ] process > NFCORE_FETCHNGS:SRA:MULTIQC... -
[-        ] process > NFCORE_FETCHNGS:SRA:CUSTOM_... -
[68/a3b0c4] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_SRATOOLS:SRATOOLS_PREFETCH (SRR14593545)` terminated with an error exit status (1) -- Execution is retried (1)
[2d/b2d3a5] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_SRATOOLS:SRATOOLS_PREFETCH (SRR14709033)` terminated with an error exit status (1) -- Execution is retried (1)
[9a/02508e] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_SRATOOLS:SRATOOLS_PREFETCH (SRR12848126)` terminated with an error exit status (1) -- Execution is retried (1)
[29/3ce30d] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_SRATOOLS:SRATOOLS_PREFETCH (SRR14709033)` terminated with an error exit status (1) -- Execution is retried (2)
[c1/c5b350] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_SRATOOLS:SRATOOLS_PREFETCH (SRR14593545)` terminated with an error exit status (1) -- Execution is retried (2)
[b3/0c2b7d] NOTE: Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_SRATOOLS:SRATOOLS_PREFETCH (SRR12848126)` terminated with an error exit status (1) -- Execution is retried (2)
Error executing process > 'NFCORE_FETCHNGS:SRA:SRA_FASTQ_SRATOOLS:SRATOOLS_PREFETCH (SRR14709033)'

Caused by:
  Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_SRATOOLS:SRATOOLS_PREFETCH (SRR14709033)` terminated with an error exit status (1)

Command executed:

  eval "$(vdb-config -o n NCBI_SETTINGS | sed 's/[" ]//g')"
  if [[ ! -f "${NCBI_SETTINGS}" ]]; then
      mkdir -p "$(dirname "${NCBI_SETTINGS}")"
      printf '/LIBS/GUID = "b6aa337c-d642-4239-a4ab-552792ae78b2"\n/libs/cloud/report_instance_identity = "true"\n' > "${NCBI_SETTINGS}"
  fi

  retry_with_backoff.sh prefetch \
       \
      --progress \
      SRR14709033

  vdb-validate SRR14709033

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_FETCHNGS:SRA:SRA_FASTQ_SRATOOLS:SRATOOLS_PREFETCH":
      sratools: $(prefetch --version 2>&1 | grep -Eo '[0-9.]+')
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  .command.sh: line 2: vdb-config: command not found
  .command.sh: line 3: NCBI_SETTINGS: unbound variable

Work dir:
  /home/dalin/nf_core/work/6b/3f1324636644f4b5afbc809ce41f5f

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


WARN: To render the execution DAG in the required format it is required to install Graphviz -- See http://www.graphviz.org for more info.

Relevant files

No response

System information

nextflow: v22.04
Hardware: Desktop
Container: Docker
OS: Ubuntu 22.04
nf-core/fetch ngs: v1.5

[Midnighter]

You need to separate profiles by comma without any spaces:

nextflow run nf-core/fetchngs -profile test,docker

[drpatelh]

Assuming the fix above resolved the issue. In the future it may be easier to join the #fetchngs channel on nf-core Slack to get real-time help. You can join via the link below:
https://nf-co.re/join