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Error in uploading workflow #150

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VGPReys opened this issue Apr 24, 2024 · 3 comments
Open

Error in uploading workflow #150

VGPReys opened this issue Apr 24, 2024 · 3 comments

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@VGPReys
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VGPReys commented Apr 24, 2024

Got the following error(s) while trying to upload a workflow in workflow builder (http://localhost:8080/builder):

Workflow archive failed to load.

  • Error in nodes[0]: must have node name belonging to known nodes
  • Error in nodes[5]: must NOT have additional properties: tolerance
  • Error in nodes[7]: must NOT have additional properties: tolerance

here is the workflow.cfg file content:

# ====================================================================
# Antibody-antigen docking example with restraints from the antibody
# paratope to the NMR-identified epitope on the antigen 
# ====================================================================

# directory in which the scoring will be done
run_dir = "run1-CDR-NMR-CSP"

# compute mode
mode = "local"
ncores = 50

# Self contained rundir (to avoid problems with long filename paths)
self_contained = true

# Post-processing to generate statistics and plots
postprocess = true
clean = true

molecules =  [
    "4G6K_clean.pdb",
    "4I1B_clean.pdb"
    ]

# ====================================================================
# Parameters for each stage are defined below, prefer full paths
# ====================================================================
[topoaa]

[rigidbody]
# CDR to NMR epitope ambig restraints
ambig_fname = "ambig-paratope-NMR-epitope.tbl"
# Restraints to keep the antibody chains together
unambig_fname = "antibody-unambig.tbl"
sampling = 50

[caprieval]
reference_fname = "4G6M_matched.pdb"

[seletop]
# Selection of the top 40 best scoring complexes
select = 40

[flexref]
tolerance = 5
# CDR to NMR epitope ambig restraints
ambig_fname = "ambig-paratope-NMR-epitope.tbl"
# Restraints to keep the antibody chains together
unambig_fname = "antibody-unambig.tbl"

[caprieval]
reference_fname = "4G6M_matched.pdb"

[emref]
tolerance = 5
# CDR to NMR epitope ambig restraints
ambig_fname = "ambig-paratope-NMR-epitope.tbl"
# Restraints to keep the antibody chains together
unambig_fname = "antibody-unambig.tbl"

[caprieval]
reference_fname = "4G6M_matched.pdb"

[clustfcc]
plot_matrix = true

[seletopclusts]
# Selection of the top 4 best scoring complexes from each cluster
top_models = 4

[caprieval]
reference_fname = "4G6M_matched.pdb"

[contactmap]

# ====================================================================
@VGPReys
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VGPReys commented Apr 24, 2024

After multiple tries, I realized that I only got the error while logged in as user.
As admin, it works fine !

@VGPReys
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VGPReys commented Apr 24, 2024

Also with guru expertise level, same error occurs.

@sverhoeven
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Seems like you are using the builder from inside the haddock3-webapp. The webapp does some massaging of the catalog, which might be the cause.

Did you try same workflow in https://i-vresse-workflow-builder.netlify.app/ with guru or expert catalog?

Can you give the zip archive, so I can try to reproduce the error?

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