# Issue with Prolonged Runtime in HADDOCK2.5 During NOE Analysis

**URL:** <https://ask.bioexcel.eu/t/issue-with-prolonged-runtime-in-haddock2-5-during-noe-analysis/5173>\
**Category:** HADDOCK\
**Created:** [July 5, 2024, 7:01am UTC](https://ask.bioexcel.eu/t/issue-with-prolonged-runtime-in-haddock2-5-during-noe-analysis/5173 "2024-07-05T07:01:59Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![zhuyaojun](https://avatars.discourse-cdn.com/v4/letter/z/f9ae1b/32.png) [@zhuyaojun](https://ask.bioexcel.eu/u/zhuyaojun)\
**Post date:** [July 5, 2024, 7:02am UTC](https://ask.bioexcel.eu/t/issue-with-prolonged-runtime-in-haddock2-5-during-noe-analysis/5173/1 "2024-07-05T07:02:00Z")

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Dear HADDOCK Support Team,

I hope this message finds you well. I am currently using HADDOCK2.5 for protein-protein docking simulations.

During the docking process, I encountered an issue where the system remains in the “waiting for the NOE analysis file…” state for over three hours. Upon checking the CPU usage, I observed that it remains below 20%, which seems unusually low for such a computational task.

I have attached a screenshot showing the current status.

Could you kindly provide guidance on whether this behavior is expected or if there might be an underlying issue that needs to be addressed? Any suggestions on how to resolve this and optimize the performance would be greatly appreciated.

Thank you very much for your time and assistance. I look forward to your response.

Best regards,

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<div class="post-metadata">

**Author:** ![zhuyaojun](https://avatars.discourse-cdn.com/v4/letter/z/f9ae1b/32.png) [@zhuyaojun](https://ask.bioexcel.eu/u/zhuyaojun)\
**Post date:** [July 5, 2024, 7:08am UTC](https://ask.bioexcel.eu/t/issue-with-prolonged-runtime-in-haddock2-5-during-noe-analysis/5173/2 "2024-07-05T07:08:34Z")

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![image](https://europe1.discourse-cdn.com/flex013/uploads/bioexcel/original/2X/f/f6c35b53b7dc4ca26deb526f5f7dbb34e6db6016.png)

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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:** [July 5, 2024, 7:26am UTC](https://ask.bioexcel.eu/t/issue-with-prolonged-runtime-in-haddock2-5-during-noe-analysis/5173/3 "2024-07-05T07:26:58Z")

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Looks like some of the post-processing NOE analysis is failing…

The (old) script used is a combination of awk and csh. Make sure those are installed on your system.

To make it proceed what you can do is:

touch structures/it1/analysis/NOE\_DONE  
touch structures/it1/water/analysis/NOE\_DONE

Note that by default we don’t perform anymore a full analysis but only the clustering.

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<div class="post-metadata">

**Author:** ![zhuyaojun](https://avatars.discourse-cdn.com/v4/letter/z/f9ae1b/32.png) [@zhuyaojun](https://ask.bioexcel.eu/u/zhuyaojun)\
**Post date:** [July 5, 2024, 8:02am UTC](https://ask.bioexcel.eu/t/issue-with-prolonged-runtime-in-haddock2-5-during-noe-analysis/5173/4 "2024-07-05T08:02:50Z")

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Thank you very much for your help.