# Stuck on "waiting for the matrix file in it1/analysis" (Local installation on Ubuntu)

**URL:** <https://ask.bioexcel.eu/t/stuck-on-waiting-for-the-matrix-file-in-it1-analysis-local-installation-on-ubuntu/70>\
**Category:** HADDOCK\
**Created:** [April 21, 2016, 12:17pm UTC](https://ask.bioexcel.eu/t/stuck-on-waiting-for-the-matrix-file-in-it1-analysis-local-installation-on-ubuntu/70 "2016-04-21T12:17:52Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![Rui\_Almeida](https://avatars.discourse-cdn.com/v4/letter/r/a6a055/32.png) [@Rui\_Almeida](https://ask.bioexcel.eu/u/Rui_Almeida)\
**Post date:** [April 21, 2016, 12:17pm UTC](https://ask.bioexcel.eu/t/stuck-on-waiting-for-the-matrix-file-in-it1-analysis-local-installation-on-ubuntu/70/1 "2016-04-21T12:17:52Z")

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Hello  
I am running HADDOCK2.2 on Ubuntu 15.04 (local installation).  
After a while, the algorithm seems to get stuck on this part: “waiting for the matrix file in it1/analysis”

Prior to this, the following awk errors occurred:

“awk: count\_hbonds.awk: line 53: syntax error at or near \*”

\*.out files in …/it1/analysis include:  
print\_dih  
print\_dist\_all  
print\_dist\_hbonds  
print\_dist\_noes  
print\_noe  
print\_noe\_all  
print\_noe\_ambig  
print\_noe\_unambig

Plus the following \*out.gz  
edesolv  
ene-residue  
energy  
fcc  
print\_dani  
print\_geom  
print\_hbonds  
print\_nb  
print\_noes  
print\_rg  
print\_sani  
print\_vean  
print\_xpcs  
print\_xrdc.

Additionally, the following DONE files are also present:

DIH\_DONE  
DONE  
ENE\_DONE  
HBONDS\_DONE  
NB\_DONE  
NOE\_DONE

Am I missing something?

Any help would be greatly appreciated.

Best regards  
Rui Almeida.

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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 21, 2016, 12:25pm UTC](https://ask.bioexcel.eu/t/stuck-on-waiting-for-the-matrix-file-in-it1-analysis-local-installation-on-ubuntu/70/2 "2016-04-21T12:25:16Z")

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Did you compile the analysis programs coming with HADDOCK?  
I.e. did you run make in the main HADDOCK install dir?

Also which clustering method are you using? FCC or RMSD?

Calculating the RMSD matrix can take a few hours depending on the size of your system and number of models. FCC should be much faster.

If you want it to proceed, a simple solution would be to create the MTX\_DONE file in the it1/analysis directory (assuming you are running HADDOCK2.2):

```auto
touch structure/it1/analysis/MTX_DONE

```

This should make HADDOCK continue, but won’t fix the clustering issue.

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**Author:** ![Rui\_Almeida](https://avatars.discourse-cdn.com/v4/letter/r/a6a055/32.png) [@Rui\_Almeida](https://ask.bioexcel.eu/u/Rui_Almeida)\
**Post date:** [April 21, 2016, 12:43pm UTC](https://ask.bioexcel.eu/t/stuck-on-waiting-for-the-matrix-file-in-it1-analysis-local-installation-on-ubuntu/70/3 "2016-04-21T12:43:37Z")

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Dear Alexandre  
I had indeed run make in the haddock installation directory.  
Creating MTX\_DONE solved the issue.

Thank you for your help.  
Rui A.