PAP Structural workflow

Hi,
Does anyone else have trouble running the PAP structural workflow?
For me it has been running for days now, and then it is now halted at #14: ‘MGA to GFF3’

I have just uploaded my fasta file and run the workflow, with all default settings except for the ‘Create or Update organism’.

/Lene

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Hi @lsmr

I’m not sure what this means. Is the job still running for a long time? Or, did it error? Or, did downstream tools end up in a paused state? Have you checked the last successful job’s dataset to see if it contains data with no metadata warnings?

A few more details would also help if that doesn’t solve your problem:

  1. What server are you working at? URL?
  2. Public Galaxy or private?
  3. Share link to the workflow. If associated with a tutorial, share a link to that as well will help with context.

Thanks!

hi,
it did error when trying to run ‘MGA to GFF3’ on Fasta file input without description (first step in the workflow) and on ‘MetaGeneAnnotator’.
I tried to re-run it, and now it error at the ‘MetaGeneAnnotator’:
Fatal error: Exit code 127 ()
/galaxy/database/jobs_directory/000/183/183563/tool_script.sh: line 9: mga_linux_x64: command not found

It is some of the very first steps in the workflow that errors, and all I do is to upload my fasta file for it to use.

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It is still not clear where you are working, where the tool was sourced, and what workflow you are using.

It appears to be your own local Galaxy and I didn’t find that tool in the ToolShed https://usegalaxy.org/toolshed.

Please clarify as requested above:

This might be the workflow you are using: https://cpt.tamu.edu/galaxy-pub/u/cory-maughmer/w/pap-2019-structural-workflow-v810

If the workflow is erroring at different steps, the jobs may be exceeding the computational resources where you are working. Or something else is wrong. You’ll need to contact their support – many of these tools are custom for this domain-specific server.

Each public Galaxy is independently administered. If that server accepts bug reports, send one in. Or you can contact them directly. Some Galaxy servers post contact on the home page and/or here: https://galaxyproject.org/use/.

Contact for this server (and the workflow author) happen to be posted on the homepage of the server: https://cpt.tamu.edu/galaxy-pub plus also here https://galaxyproject.org/use/center-for-phage-technology-cpt/.

Thank you.