Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Per module/subworkflow tags.yml file #212

Merged
merged 6 commits into from
Oct 10, 2023

fixup

051588c
Select commit
Loading
Failed to load commit list.
Refresh
Sign in for the full log view
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 atacseq

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Parameters: --nf_core_pipeline atacseq 

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
    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/7c7c71c862b2f925a2446f34a598cef7/work/ed/4e84e7b5a28159f4a4de2f946db527

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

 -- Check '/tmp/tests/7c7c71c862b2f925a2446f34a598cef7/meta/nextflow.log' file for details
WARN: Killing running tasks (1)
Nextflow stderr:
View more details on GitHub Actions