# Problem with Analysis in Local HADDOCK set-up

**URL:** <https://ask.bioexcel.eu/t/problem-with-analysis-in-local-haddock-set-up/3653>\
**Category:** HADDOCK\
**Created:** [April 7, 2022, 9:47pm UTC](https://ask.bioexcel.eu/t/problem-with-analysis-in-local-haddock-set-up/3653 "2022-04-07T21:47:55Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![ananyam](https://avatars.discourse-cdn.com/v4/letter/a/da6949/32.png) [@ananyam](https://ask.bioexcel.eu/u/ananyam)\
**Post date:** [April 7, 2022, 9:47pm UTC](https://ask.bioexcel.eu/t/problem-with-analysis-in-local-haddock-set-up/3653/1 "2022-04-07T21:47:55Z")

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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?

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**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\
**Post date:** [April 8, 2022, 7:41am UTC](https://ask.bioexcel.eu/t/problem-with-analysis-in-local-haddock-set-up/3653/2 "2022-04-08T07:41:28Z")

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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
- …

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<div class="post-metadata">

**Author:** ![ananyam](https://avatars.discourse-cdn.com/v4/letter/a/da6949/32.png) [@ananyam](https://ask.bioexcel.eu/u/ananyam)\
**Post date:** [April 8, 2022, 1:34pm UTC](https://ask.bioexcel.eu/t/problem-with-analysis-in-local-haddock-set-up/3653/3 "2022-04-08T13:34:40Z")

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Hello,

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.

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<div class="post-metadata">

**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\
**Post date:** [April 8, 2022, 2:15pm UTC](https://ask.bioexcel.eu/t/problem-with-analysis-in-local-haddock-set-up/3653/4 "2022-04-08T14:15:12Z")

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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)