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Per module/subworkflow tags.yml file #641

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Per module/subworkflow tags.yml file

Per module/subworkflow tags.yml file #641

GitHub Actions / JUnit Test Report failed Oct 10, 2023 in 0s

1 tests run, 0 passed, 0 skipped, 1 failed.

Annotations

Check failure on line 1 in Parameters: --nf_core_pipeline viralrecon

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Parameters: --nf_core_pipeline viralrecon 

Assertion failed: 

2 of 2 assertions failed
Raw output 
Nextflow stdout:

ERROR ~ Error executing process > 'SRA:SRA_FASTQ_FTP (DRX024467_DRR026872)'

Caused by:
  Process `SRA:SRA_FASTQ_FTP (DRX024467_DRR026872)` terminated with an error exit status (28)

Command executed:

  curl \
      --retry 5 --continue-at - --max-time 1200 \
      -L ftp.sra.ebi.ac.uk/vol1/fastq/DRR026/DRR026872/DRR026872.fastq.gz \
      -o DRX024467_DRR026872.fastq.gz
  
  echo "515e5448c55e054113c4a22df5f62791  DRX024467_DRR026872.fastq.gz" > DRX024467_DRR026872.fastq.gz.md5
  md5sum -c DRX024467_DRR026872.fastq.gz.md5
  
  cat <<-END_VERSIONS > versions.yml
  "SRA:SRA_FASTQ_FTP":
      curl: $(echo $(curl --version | head -n 1 | sed 's/^curl //; s/ .*$//'))
  END_VERSIONS

Command exit status:
  28

Command output:
  (empty)

Command error:
    % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                   Dload  Upload   Total   Spent    Left  Speed
  
    0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
    0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  curl: (28) Timeout was reached
  Warning: Problem : timeout. Will retry in 1 seconds. 5 retries left.
  
    0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
    0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
    0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  curl: (28) Timeout was reached
  Warning: Problem : timeout. Will retry in 2 seconds. 4 retries left.
  
    0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
    0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  curl: (28) Timeout was reached
  Warning: Problem : timeout. Will retry in 4 seconds. 3 retries left.
  
    0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
    0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  curl: (28) Timeout was reached
  Warning: Problem : timeout. Will retry in 8 seconds. 2 retries left.
  
    0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
    0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  curl: (28) Timeout was reached
  Warning: Problem : timeout. Will retry in 16 seconds. 1 retries left.
  
    0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
    0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  curl: (28) Timeout was reached

Work dir:
  /tmp/tests/b6119d1bc44a05070663cabe6d10e8c3/work/21/cf3072839ed0285e363124f17c7a3e

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

 -- Check '/tmp/tests/b6119d1bc44a05070663cabe6d10e8c3/meta/nextflow.log' file for details
Nextflow stderr:

Nextflow 23.09.2-edge is available - Please consider updating your version to it
View more details on GitHub Actions