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Per module/subworkflow tags.yml file #212

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merged 6 commits into from
Oct 10, 2023

fixup

051588c
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Merged

Per module/subworkflow tags.yml file #212

fixup
051588c
Select commit
Loading
Failed to load commit list.
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 taxprofiler

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Parameters: --nf_core_pipeline taxprofiler 

Assertion failed: 

2 of 2 assertions failed
Raw output 
Nextflow stdout:

WARN: There's no process matching config selector: CUSTOM_DUMPSOFTWAREVERSIONS
ERROR ~ Error executing process > 'SRA:SRA_FASTQ_FTP (DRX026011_DRR028935)'

Caused by:
  Process `SRA:SRA_FASTQ_FTP (DRX026011_DRR028935)` 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/DRR028/DRR028935/DRR028935_1.fastq.gz \
      -o DRX026011_DRR028935_1.fastq.gz
  
  echo "cc01df82a9354bb6b3be93483b20c35a  DRX026011_DRR028935_1.fastq.gz" > DRX026011_DRR028935_1.fastq.gz.md5
  md5sum -c DRX026011_DRR028935_1.fastq.gz.md5
  
  curl \
      --retry 5 --continue-at - --max-time 1200 \
      -L ftp.sra.ebi.ac.uk/vol1/fastq/DRR028/DRR028935/DRR028935_2.fastq.gz \
      -o DRX026011_DRR028935_2.fastq.gz
  
  echo "941c9998d746416dad53c94c480ddf30  DRX026011_DRR028935_2.fastq.gz" > DRX026011_DRR028935_2.fastq.gz.md5
  md5sum -c DRX026011_DRR028935_2.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
  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
    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/373310d47d878172dd887ebfbc32cceb/work/d5/70f97871921951f28e76c8906445db

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

 -- Check '/tmp/tests/373310d47d878172dd887ebfbc32cceb/meta/nextflow.log' file for details
WARN: Killing running tasks (1)
Nextflow stderr:
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