# Your HADDOCK run has failed
**URL:** https://ask.bioexcel.eu/t/your-haddock-run-has-failed/1558
**Category:** HADDOCK
**Created:** [May 7, 2019, 5:38pm UTC](https://ask.bioexcel.eu/t/your-haddock-run-has-failed/1558 "2019-05-07T17:38:43Z")
**Posts on this page:** 13
**Page:** 1
### Author:  [@ajaniharesh](https://ask.bioexcel.eu/u/ajaniharesh)
#### Post date: [May 7, 2019, 5:38pm UTC](https://ask.bioexcel.eu/t/your-haddock-run-has-failed/1558/1 "2019-05-07T17:38:43Z")
Hi Prof. Bonvin,
I am writing to you because since the last week jobs continuously fail in predict interface. I already checked the pdb file. It seems to look good. See below for error.
our HADDOCK run has encountered errors and was aborted. Go to [http://milou.science.uu.nl/serviceresults/HADDOCK2.2/5785077997/test\_prect](http://milou.science.uu.nl/serviceresults/HADDOCK2.2/5785077997/test_prect) for more details.
Note that HADDOCK results are deleted after one week.
Regards,
Haresh
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### Author:  [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)
#### Post date: [May 7, 2019, 6:35pm UTC](https://ask.bioexcel.eu/t/your-haddock-run-has-failed/1558/2 "2019-05-07T18:35:42Z")
We had last week issues with some grid sites on which our jobs are running.
The situation should be back to normal but this might have affected ongoing runs.
We did notify users about it.
When did you submit the last runs that failed?
I suggest you simply resubmit those.
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### Author:  [@ajaniharesh](https://ask.bioexcel.eu/u/ajaniharesh)
#### Post date: [May 7, 2019, 7:06pm UTC](https://ask.bioexcel.eu/t/your-haddock-run-has-failed/1558/3 "2019-05-07T19:06:12Z")
Thanks Prof. Bonvin for your reply.
Yesterday, I have submitted. I submitted two jobs one with easy interface and finished. but, second was on prediction interface, that job was failed. I tried day before yesterday as well on prediction interface that on was also failed.
Haresh
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### Author:  [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)
#### Post date: [May 7, 2019, 9:00pm UTC](https://ask.bioexcel.eu/t/your-haddock-run-has-failed/1558/4 "2019-05-07T21:00:57Z")
Ok - please try again and let us know if the prediction one now goes through
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### Author:  [@ajaniharesh](https://ask.bioexcel.eu/u/ajaniharesh)
#### Post date: [May 8, 2019, 1:15pm UTC](https://ask.bioexcel.eu/t/your-haddock-run-has-failed/1558/5 "2019-05-08T13:15:21Z")
Hello Prof. Bonvin
Sorry, again job failed those I have submitted yesterday on Prediction interface. see the below detail.
Your HADDOCK run has encountered errors and was aborted. Go to [http://milou.science.uu.nl/serviceresults/HADDOCK2.2/5785077997/test-vhl-prect](http://milou.science.uu.nl/serviceresults/HADDOCK2.2/5785077997/test-vhl-prect) for more details.
Note that HADDOCK results are deleted after one week.
Kind regards,
The HADDOCK server
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### Author:  [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)
#### Post date: [May 8, 2019, 8:07pm UTC](https://ask.bioexcel.eu/t/your-haddock-run-has-failed/1558/6 "2019-05-08T20:07:18Z")
Seems running fine now:
[https://milou.science.uu.nl/serviceresults/HADDOCK2.2/1111111111/test-vhl-prect/](https://milou.science.uu.nl/serviceresults/HADDOCK2.2/1111111111/test-vhl-prect/)
so far so good.
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### Author:  [@Marija](https://ask.bioexcel.eu/u/Marija)
#### Post date: [October 17, 2020, 7:10pm UTC](https://ask.bioexcel.eu/t/your-haddock-run-has-failed/1558/7 "2020-10-17T19:10:28Z")
Dear Professor Bonvin,
I would like to ask why water refinement jobs submitted with “submit” option at HADDOCK2.4 web-server fail. I do not get any error message but I have noticed that number of both, structures\_0 and structures\_1, are set to 0 in job\_params.json, although I was setting the values to 20.
The same structures submitted to Multi-body interface of HD2.2 or Refinement interface of HD2.4 are getting refined without any error.
Here are two links to the failed jobs:
[https://wenmr.science.uu.nl/haddock2.4/run/5046414253/26300-closed\_model\_ABC/job\_params.json](https://wenmr.science.uu.nl/haddock2.4/run/5046414253/26300-closed_model_ABC/job_params.json)
[https://wenmr.science.uu.nl/haddock2.4/run/5046414253/26131-closed\_phys\_chem\_1/job\_params.json](https://wenmr.science.uu.nl/haddock2.4/run/5046414253/26131-closed_phys_chem_1/job_params.json)
Thank you very much.
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### Author:  [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)
#### Post date: [October 18, 2020, 7:36am UTC](https://ask.bioexcel.eu/t/your-haddock-run-has-failed/1558/8 "2020-10-18T07:36:13Z")
The number of structures is indeed set to 0, which is strange.
Can you describe all the steps you did for the submission? Which parameter did you change…?
So that we can try to reproduce it.
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### Author:  [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)
#### Post date: [October 18, 2020, 7:38am UTC](https://ask.bioexcel.eu/t/your-haddock-run-has-failed/1558/9 "2020-10-18T07:38:36Z")
PS: Are you following the following recipe?
[https://www.bonvinlab.org/software/haddock2.4/tips/advanced\_refinement/](https://www.bonvinlab.org/software/haddock2.4/tips/advanced_refinement/)
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### Author:  [@Marija](https://ask.bioexcel.eu/u/Marija)
#### Post date: [October 18, 2020, 8:48am UTC](https://ask.bioexcel.eu/t/your-haddock-run-has-failed/1558/10 "2020-10-18T08:48:13Z")
Thank you very much for your reply.
Yes exactly, I am following the recipe exactly as described here: [https://www.bonvinlab.org/software/haddock2.4/tips/advanced\_refinement/](https://www.bonvinlab.org/software/haddock2.4/tips/advanced_refinement/)
I am setting the following parameters to 20, but after submission they are set to 0:
Number of structures for rigid body docking
Number of structures for semi-flexible refinement
Number of structures for the final refinement
Number of structures to analyze
I just tried to submit another molecule and the run failed again probably due to the same reason:
[https://wenmr.science.uu.nl/haddock2.4/run/5046414253/26343-open\_model/job\_params.json](https://wenmr.science.uu.nl/haddock2.4/run/5046414253/26343-open_model/job_params.json)
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### Author:  [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)
#### Post date: [October 18, 2020, 10:07am UTC](https://ask.bioexcel.eu/t/your-haddock-run-has-failed/1558/11 "2020-10-18T10:07:56Z")
Well - I can not reproduce your problem. See:
[https://bianca.science.uu.nl/haddock2.4/run/1111111111/26345-test-refinement/job\_params.json](https://bianca.science.uu.nl/haddock2.4/run/1111111111/26345-test-refinement/job_params.json)
BUT it indeed happens if following exactly the recipe:
- _Multiply the number of calculated structures by all combinations_ → True
If you leave it to false it works fine.
So a bug in the server machinery.
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### Author:  [@Marija](https://ask.bioexcel.eu/u/Marija)
#### Post date: [October 18, 2020, 11:26am UTC](https://ask.bioexcel.eu/t/your-haddock-run-has-failed/1558/12 "2020-10-18T11:26:17Z")
Thank you very much for your help.
I have restarted my jobs leaving the option to false and now it looks fine.
I am not sure what this option (_Multiply the number of calculated structures by all combinations_) exactly means, which structures will be multiplied. Can this option if it is left at false have a big influence on the resulting structures?
Do you think this bug can be fixed soon?
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### Author:  [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)
#### Post date: [October 18, 2020, 12:00pm UTC](https://ask.bioexcel.eu/t/your-haddock-run-has-failed/1558/13 "2020-10-18T12:00:31Z")
The option is meant if you provide an ensemble of starting structures - and it works if an ensemble is provided, but we have a bug if turned on for a single structure
Should be fixed soon