Problem with Analysis in Local HADDOCK set-up

Hello Everyone,

I am new to HADDOCK and am trying to use it for protein-protein docking with PCS values. Initially the run seems to work well, however when it moves onto the cluster analysis step i get the following error message: waiting for “matrix/it1/analysis” , and the run stalls. All of the models for the it0, it1, and water steps are generated, but a majority of the analysis steps - ranging from RMSD calculations, pcs error output etc., never completes.

Has anyone ever encountered this error?

What is the content of the analysis directory?

There might be several reasons why it is pending, e.g.:

  • a problem with the it1 models
  • problems with the haddock installation


The analysis directory contains:

  1. fitted pdb files for the models generated
  2. the reduced coordinates file (which puts the PCS energy at 0)
  3. the fcc.out.gz file (which when opened states “python: No match”
  4. the get_average.out.gz file
  5. the iteration.cns file (which when opened is comprised of two lines stating module (iteration 1) and evaluate (&iteration1)
  6. the rmsave.disp file
  7. the rmsdseq.disp file

Thank you.

Point 3 below is your problem

  1. the fcc.out.gz file (which when opened states “python: No match”

There must be a problem with the python version used to run the contact analysis / clustering.
It does required python2.7

In the run dir you should see a …fcc…job file.
Try executing manually. If working there should be .contacts files appearing in the analysis directory.

Also check that the contact_fcc executable is present in the tools directory (should have been compiled when you installed haddock2.4)