Failure to download README from osf.io

[rhysnewell]

Hi there,

I'm just trying to get MUFFIN to run on my universities HPC but I seem to be hitting a wall. I think out firewall prevents access to https://osf.io, so the pipeline fails almost immediately when it tries to download the README documentation.

Command used:

NXF_VER=20.10.0 nextflow run RVanDamme/MUFFIN --output test_dir  --cpus 8 --memory 32g -profile local,singularity --illumina subset/subset_ill/ --ont subset/subset_ont/

Error:

Error executing process > 'readme_output'

Caused by:
  Process `readme_output` terminated with an error exit status (5)

Command executed:

  wget https://osf.io/a6hru/download -O README_output.txt

Command exit status:
  5

Command output:
  (empty)

Command error:
  WARNING: While bind mounting '/lustre/scratch/microbiome/n10853499/00-rosella_testing/02-activated_sludge/assembly/work/14/165f06a9cd1ef4d8a7d54c15f26b3e:/lustre/scratch/microbiome/n10853499/00-rosella_testing/02-activated_sludge/assembly/work/14/165f06a9cd1ef4d8a7d54c15f26b3e': destination is already in the mount point list
  --2022-02-10 12:37:36--  https://osf.io/a6hru/download
  Resolving osf.io (osf.io)... 35.190.84.173
  Connecting to osf.io (osf.io)|35.190.84.173|:443... connected.
  ERROR: The certificate of ‘osf.io’ is not trusted.
  ERROR: The certificate of ‘osf.io’ has expired.

Work dir:
  /lustre/scratch/microbiome/n10853499/00-rosella_testing/02-activated_sludge/assembly/work/14/165f06a9cd1ef4d8a7d54c15f26b3e

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`

Is it possible to skip this step? I couldn't find anything in the documentation, but it seems like others might run into a similar issue if it is indeed a firewall problem.

Cheers, Rhys

[replikation]

hi could you try the latest master. i just added the --no-check-certificate to all wget commands. should work now

[rhysnewell]

Thanks, I think that has fixed it. It's still running at the moment, but I'll let you know when it finishes

[rhysnewell]

Cool, finished up with no error just after I posted that. Closing now