'NoneType' object has no attribute 'identificator' #1181
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bug
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how to resolve it, pls help |
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hi @Harshilwalia777 , are you running the most recent version of the code? if that is the case, please provide us the used workflow and the input files. |
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i have used latest |
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i have used examples .cfg file |
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I am using latest haddock 3 by using pip Install Haddock 3. Test it again
by reinstalling it in another environment using conda.
On Thu, 12 Dec 2024, 14:02 Alexandre Bonvin, ***@***.***>
wrote:
… Results are only kept for two
weeks…================================= Prof. A.M.J.J. Bonvin | Faculty of
Science Utrecht University | ***@***.*** | T: +31 30
2533859 =================================On 11 Dec 2024, at 18:13,
Harshilwalia777 ***@***.***> wrote:
how to resolve it, pls help
—Reply to this email directly, view it on GitHub, or unsubscribe.You are
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You are receiving this because you authored the thread.Message ID:
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Please provide the output of the git command I gave in my previous message? Is it the same I provided?
If not, rather try in your conda environment the following installation procedure:
```
git clone https://github.com/haddocking/haddock3.git
cd haddock3
pip install .
```
|
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[2024-12-12 16:40:45,738 contmap INFO] Generated report file:
ContactMapReport.html
[2024-12-12 16:40:45,743 __init__ INFO] Module [contactmap] finished.
[2024-12-12 16:40:45,743 __init__ INFO] [contactmap] took 0 seconds
[2024-12-12 16:40:45,743 cli_analyse INFO] Running haddock3-analyse on ./,
modules [], with top_cluster = 10
[2024-12-12 16:40:45,754 cli_analyse INFO] Created directory:
/home/root777/haddock3/examples/analysis/test_contmap/analysis
[2024-12-12 16:40:45,754 cli_analyse INFO] Reading input run directory
[2024-12-12 16:40:45,754 cli_analyse INFO] selected steps: 0_topoaa,
1_rigidbody, 2_clustfcc, 3_contactmap
[2024-12-12 16:40:45,754 cli_analyse INFO] Analysing step 0_topoaa
[2024-12-12 16:40:45,755 cli_analyse WARNING] Could not execute the
analysis for step 0_topoaa. The following error occurred 'dict' object has
no attribute 'rel_path'
[2024-12-12 16:40:45,755 cli_analyse INFO] Analysing step 1_rigidbody
[2024-12-12 16:40:45,757 cli_unpack INFO] Unpacking '../1_rigidbody' folder
[2024-12-12 16:40:45,758 libtimer INFO] unpacking took 0 seconds
[2024-12-12 16:40:45,788 capri INFO] Found previous CNS step: 1_rigidbody
[2024-12-12 16:40:46,088 capri INFO] Saved scoring weights to:
weights_params.json
[2024-12-12 16:40:46,088 __init__ INFO] [caprieval] No reference was given.
Using the structure with the lowest score from previous step
[2024-12-12 16:40:46,210 libutil INFO] Selected 5 cores to process 20 jobs,
with 16 maximum available cores.
[2024-12-12 16:40:46,211 libparallel INFO] Using 5 cores
[2024-12-12 16:40:46,262 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,262 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,263 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,265 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,270 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,288 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,290 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,292 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,292 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,296 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,313 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,315 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,316 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,316 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,321 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,336 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,339 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,342 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,342 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,344 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,347 libparallel INFO] 20 tasks finished
[2024-12-12 16:40:46,348 cli_analyse WARNING] Could not execute the
analysis for step 1_rigidbody. The following error occurred 'NoneType'
object has no attribute 'identificator'
[2024-12-12 16:40:46,348 cli_analyse INFO] Analysing step 2_clustfcc
[2024-12-12 16:40:46,350 cli_unpack INFO] Unpacking '../1_rigidbody' folder
[2024-12-12 16:40:46,351 libtimer INFO] unpacking took 0 seconds
[2024-12-12 16:40:46,373 capri INFO] Found previous CNS step: 1_rigidbody
[2024-12-12 16:40:46,646 capri INFO] Saved scoring weights to:
weights_params.json
[2024-12-12 16:40:46,646 __init__ INFO] [caprieval] No reference was given.
Using the structure with the lowest score from previous step
[2024-12-12 16:40:46,744 libutil INFO] Selected 5 cores to process 17 jobs,
with 16 maximum available cores.
[2024-12-12 16:40:46,745 libparallel INFO] Using 5 cores
[2024-12-12 16:40:46,792 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,795 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,801 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,801 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,804 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,815 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,818 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,826 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,830 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,839 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,842 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,849 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,854 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,861 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,865 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,870 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,879 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,882 libparallel INFO] 17 tasks finished
[2024-12-12 16:40:46,883 cli_analyse WARNING] Could not execute the
analysis for step 2_clustfcc. The following error occurred 'NoneType'
object has no attribute 'identificator'
[2024-12-12 16:40:46,883 cli_analyse INFO] Analysing step 3_contactmap
[2024-12-12 16:40:46,885 cli_unpack INFO] Unpacking '../1_rigidbody' folder
[2024-12-12 16:40:46,886 libtimer INFO] unpacking took 0 seconds
[2024-12-12 16:40:46,907 capri INFO] Found previous CNS step: 1_rigidbody
[2024-12-12 16:40:47,177 capri INFO] Saved scoring weights to:
weights_params.json
[2024-12-12 16:40:47,177 __init__ INFO] [caprieval] No reference was given.
Using the structure with the lowest score from previous step
[2024-12-12 16:40:47,272 libutil INFO] Selected 5 cores to process 17 jobs,
with 16 maximum available cores.
[2024-12-12 16:40:47,273 libparallel INFO] Using 5 cores
[2024-12-12 16:40:47,314 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:47,319 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:47,323 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:47,326 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:47,329 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:47,339 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:47,342 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:47,346 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:47,351 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:47,362 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:47,365 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:47,368 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:47,374 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:47,384 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:47,387 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:47,391 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:47,397 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:47,401 libparallel INFO] 17 tasks finished
[2024-12-12 16:40:47,401 cli_analyse WARNING] Could not execute the
analysis for step 3_contactmap. The following error occurred 'NoneType'
object has no attribute 'identificator'
[2024-12-12 16:40:47,401 cli_analyse INFO] cancelling unsuccesful analysis
folders
[2024-12-12 16:40:47,402 cli_traceback INFO] Running haddock3-traceback on
./
[2024-12-12 16:40:47,402 cli_traceback INFO] Reading input run directory
[2024-12-12 16:40:47,402 cli_traceback INFO] All_steps: 0_topoaa,
1_rigidbody, 2_clustfcc, 3_contactmap
[2024-12-12 16:40:47,403 cli_traceback INFO] Modules not to be analysed:
0_topoaa, 2_clustfcc, 3_contactmap
[2024-12-12 16:40:47,403 cli_traceback INFO] Steps to trace back:
1_rigidbody
[2024-12-12 16:40:47,403 cli_traceback INFO] Created directory:
/home/root777/haddock3/examples/analysis/test_contmap/traceback
[2024-12-12 16:40:47,403 cli_traceback INFO] Tracing back step 1_rigidbody
[2024-12-12 16:40:47,408 libworkflow WARNING] Error running traceback:
Cannot convert numpy.ndarray to numpy.ndarray
[2024-12-12 16:40:47,408 clean_steps INFO] Cleaning output for '0_topoaa'
using 5 cores.
[2024-12-12 16:40:47,573 libtimer INFO] cleaning output files took 0 seconds
[2024-12-12 16:40:47,573 clean_steps INFO] Cleaning output for
'1_rigidbody' using 5 cores.
[2024-12-12 16:40:47,988 libtimer INFO] cleaning output files took 0 seconds
[2024-12-12 16:40:47,989 clean_steps INFO] Cleaning output for '2_clustfcc'
using 5 cores.
[2024-12-12 16:40:48,023 libtimer INFO] cleaning output files took 0 seconds
[2024-12-12 16:40:48,023 clean_steps INFO] Cleaning output for
'3_contactmap' using 5 cores.
[2024-12-12 16:40:48,034 libtimer INFO] cleaning output files took 0 seconds
[2024-12-12 16:40:48,035 cli INFO] This HADDOCK3 run took: 54 seconds
[2024-12-12 16:40:48,035 greetings INFO] Your feedback matters in Haddock3!
Share your experience and help us grow:
[2024-12-12 16:40:48,035 greetings INFO] GitHub issues:
https://github.com/haddocking/haddock3/issues
[2024-12-12 16:40:48,035 greetings INFO] BioExcel feedback:
https://www.bonvinlab.org/feedback
[2024-12-12 16:40:48,035 greetings INFO] BioExcel forum:
https://ask.bioexcel.eu/c/haddock/6
[2024-12-12 16:40:48,035 cli INFO] Finished at 12/12/2024 16:40:48. Tot
ziens! Dovidenia! 再见!
On Thu, 12 Dec 2024 at 14:02, Alexandre Bonvin ***@***.***>
wrote:
… Results are only kept for two
weeks…================================= Prof. A.M.J.J. Bonvin | Faculty of
Science Utrecht University | ***@***.*** | T: +31 30
2533859 =================================On 11 Dec 2024, at 18:13,
Harshilwalia777 ***@***.***> wrote:
how to resolve it, pls help
—Reply to this email directly, view it on GitHub, or unsubscribe.You are
receiving this because you are subscribed to this thread.Message ID:
***@***.***>
—
Reply to this email directly, view it on GitHub
<#1181 (comment)>,
or unsubscribe
<https://github.com/notifications/unsubscribe-auth/A6NCZIHPLIM6XTEIRPOMCFL2FFC3PAVCNFSM6AAAAABTN6YFMWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDKMZYGE4DKMBWHA>
.
You are receiving this because you authored the thread.Message ID:
***@***.***>
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same result after reinstalling it.
On Thu, 12 Dec 2024 at 16:41, Harshil Walia ***@***.***>
wrote:
… [2024-12-12 16:40:45,738 contmap INFO] Generated report file:
ContactMapReport.html
[2024-12-12 16:40:45,743 __init__ INFO] Module [contactmap] finished.
[2024-12-12 16:40:45,743 __init__ INFO] [contactmap] took 0 seconds
[2024-12-12 16:40:45,743 cli_analyse INFO] Running haddock3-analyse on ./,
modules [], with top_cluster = 10
[2024-12-12 16:40:45,754 cli_analyse INFO] Created directory:
/home/root777/haddock3/examples/analysis/test_contmap/analysis
[2024-12-12 16:40:45,754 cli_analyse INFO] Reading input run directory
[2024-12-12 16:40:45,754 cli_analyse INFO] selected steps: 0_topoaa,
1_rigidbody, 2_clustfcc, 3_contactmap
[2024-12-12 16:40:45,754 cli_analyse INFO] Analysing step 0_topoaa
[2024-12-12 16:40:45,755 cli_analyse WARNING] Could not execute the
analysis for step 0_topoaa. The following error occurred 'dict' object has
no attribute 'rel_path'
[2024-12-12 16:40:45,755 cli_analyse INFO] Analysing step 1_rigidbody
[2024-12-12 16:40:45,757 cli_unpack INFO] Unpacking '../1_rigidbody' folder
[2024-12-12 16:40:45,758 libtimer INFO] unpacking took 0 seconds
[2024-12-12 16:40:45,788 capri INFO] Found previous CNS step: 1_rigidbody
[2024-12-12 16:40:46,088 capri INFO] Saved scoring weights to:
weights_params.json
[2024-12-12 16:40:46,088 __init__ INFO] [caprieval] No reference was
given. Using the structure with the lowest score from previous step
[2024-12-12 16:40:46,210 libutil INFO] Selected 5 cores to process 20
jobs, with 16 maximum available cores.
[2024-12-12 16:40:46,211 libparallel INFO] Using 5 cores
[2024-12-12 16:40:46,262 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,262 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,263 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,265 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,270 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,288 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,290 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,292 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,292 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,296 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,313 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,315 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,316 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,316 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,321 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,336 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,339 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,342 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,342 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,344 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,347 libparallel INFO] 20 tasks finished
[2024-12-12 16:40:46,348 cli_analyse WARNING] Could not execute the
analysis for step 1_rigidbody. The following error occurred 'NoneType'
object has no attribute 'identificator'
[2024-12-12 16:40:46,348 cli_analyse INFO] Analysing step 2_clustfcc
[2024-12-12 16:40:46,350 cli_unpack INFO] Unpacking '../1_rigidbody' folder
[2024-12-12 16:40:46,351 libtimer INFO] unpacking took 0 seconds
[2024-12-12 16:40:46,373 capri INFO] Found previous CNS step: 1_rigidbody
[2024-12-12 16:40:46,646 capri INFO] Saved scoring weights to:
weights_params.json
[2024-12-12 16:40:46,646 __init__ INFO] [caprieval] No reference was
given. Using the structure with the lowest score from previous step
[2024-12-12 16:40:46,744 libutil INFO] Selected 5 cores to process 17
jobs, with 16 maximum available cores.
[2024-12-12 16:40:46,745 libparallel INFO] Using 5 cores
[2024-12-12 16:40:46,792 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,795 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,801 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,801 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,804 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,815 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,818 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,826 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,830 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,839 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,842 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,849 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,854 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,861 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,865 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,870 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,879 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:46,882 libparallel INFO] 17 tasks finished
[2024-12-12 16:40:46,883 cli_analyse WARNING] Could not execute the
analysis for step 2_clustfcc. The following error occurred 'NoneType'
object has no attribute 'identificator'
[2024-12-12 16:40:46,883 cli_analyse INFO] Analysing step 3_contactmap
[2024-12-12 16:40:46,885 cli_unpack INFO] Unpacking '../1_rigidbody' folder
[2024-12-12 16:40:46,886 libtimer INFO] unpacking took 0 seconds
[2024-12-12 16:40:46,907 capri INFO] Found previous CNS step: 1_rigidbody
[2024-12-12 16:40:47,177 capri INFO] Saved scoring weights to:
weights_params.json
[2024-12-12 16:40:47,177 __init__ INFO] [caprieval] No reference was
given. Using the structure with the lowest score from previous step
[2024-12-12 16:40:47,272 libutil INFO] Selected 5 cores to process 17
jobs, with 16 maximum available cores.
[2024-12-12 16:40:47,273 libparallel INFO] Using 5 cores
[2024-12-12 16:40:47,314 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:47,319 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:47,323 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:47,326 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:47,329 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:47,339 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:47,342 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:47,346 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:47,351 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:47,362 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:47,365 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:47,368 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:47,374 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:47,384 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:47,387 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:47,391 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:47,397 libparallel WARNING] Exception in task execution:
maximum recursion depth exceeded
[2024-12-12 16:40:47,401 libparallel INFO] 17 tasks finished
[2024-12-12 16:40:47,401 cli_analyse WARNING] Could not execute the
analysis for step 3_contactmap. The following error occurred 'NoneType'
object has no attribute 'identificator'
[2024-12-12 16:40:47,401 cli_analyse INFO] cancelling unsuccesful analysis
folders
[2024-12-12 16:40:47,402 cli_traceback INFO] Running haddock3-traceback on
./
[2024-12-12 16:40:47,402 cli_traceback INFO] Reading input run directory
[2024-12-12 16:40:47,402 cli_traceback INFO] All_steps: 0_topoaa,
1_rigidbody, 2_clustfcc, 3_contactmap
[2024-12-12 16:40:47,403 cli_traceback INFO] Modules not to be analysed:
0_topoaa, 2_clustfcc, 3_contactmap
[2024-12-12 16:40:47,403 cli_traceback INFO] Steps to trace back:
1_rigidbody
[2024-12-12 16:40:47,403 cli_traceback INFO] Created directory:
/home/root777/haddock3/examples/analysis/test_contmap/traceback
[2024-12-12 16:40:47,403 cli_traceback INFO] Tracing back step 1_rigidbody
[2024-12-12 16:40:47,408 libworkflow WARNING] Error running traceback:
Cannot convert numpy.ndarray to numpy.ndarray
[2024-12-12 16:40:47,408 clean_steps INFO] Cleaning output for '0_topoaa'
using 5 cores.
[2024-12-12 16:40:47,573 libtimer INFO] cleaning output files took 0
seconds
[2024-12-12 16:40:47,573 clean_steps INFO] Cleaning output for
'1_rigidbody' using 5 cores.
[2024-12-12 16:40:47,988 libtimer INFO] cleaning output files took 0
seconds
[2024-12-12 16:40:47,989 clean_steps INFO] Cleaning output for
'2_clustfcc' using 5 cores.
[2024-12-12 16:40:48,023 libtimer INFO] cleaning output files took 0
seconds
[2024-12-12 16:40:48,023 clean_steps INFO] Cleaning output for
'3_contactmap' using 5 cores.
[2024-12-12 16:40:48,034 libtimer INFO] cleaning output files took 0
seconds
[2024-12-12 16:40:48,035 cli INFO] This HADDOCK3 run took: 54 seconds
[2024-12-12 16:40:48,035 greetings INFO] Your feedback matters in
Haddock3! Share your experience and help us grow:
[2024-12-12 16:40:48,035 greetings INFO] GitHub issues:
https://github.com/haddocking/haddock3/issues
[2024-12-12 16:40:48,035 greetings INFO] BioExcel feedback:
https://www.bonvinlab.org/feedback
[2024-12-12 16:40:48,035 greetings INFO] BioExcel forum:
https://ask.bioexcel.eu/c/haddock/6
[2024-12-12 16:40:48,035 cli INFO] Finished at 12/12/2024 16:40:48. Tot
ziens! Dovidenia! 再见!
On Thu, 12 Dec 2024 at 14:02, Alexandre Bonvin ***@***.***>
wrote:
> Results are only kept for two
> weeks…================================= Prof. A.M.J.J. Bonvin | Faculty of
> Science Utrecht University | ***@***.*** | T: +31 30
> 2533859 =================================On 11 Dec 2024, at 18:13,
> Harshilwalia777 ***@***.***> wrote:
> how to resolve it, pls help
>
> —Reply to this email directly, view it on GitHub, or unsubscribe.You are
> receiving this because you are subscribed to this thread.Message ID:
> ***@***.***>
>
> —
> Reply to this email directly, view it on GitHub
> <#1181 (comment)>,
> or unsubscribe
> <https://github.com/notifications/unsubscribe-auth/A6NCZIHPLIM6XTEIRPOMCFL2FFC3PAVCNFSM6AAAAABTN6YFMWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDKMZYGE4DKMBWHA>
> .
> You are receiving this because you authored the thread.Message ID:
> ***@***.***>
>
|
|
run analysis file 'contactmap.cfg' for checking haddock3
On Thu, 12 Dec 2024 at 16:42, Harshil Walia ***@***.***>
wrote:
… same result after reinstalling it.
On Thu, 12 Dec 2024 at 16:41, Harshil Walia ***@***.***>
wrote:
> [2024-12-12 16:40:45,738 contmap INFO] Generated report file:
> ContactMapReport.html
> [2024-12-12 16:40:45,743 __init__ INFO] Module [contactmap] finished.
> [2024-12-12 16:40:45,743 __init__ INFO] [contactmap] took 0 seconds
> [2024-12-12 16:40:45,743 cli_analyse INFO] Running haddock3-analyse on
> ./, modules [], with top_cluster = 10
> [2024-12-12 16:40:45,754 cli_analyse INFO] Created directory:
> /home/root777/haddock3/examples/analysis/test_contmap/analysis
> [2024-12-12 16:40:45,754 cli_analyse INFO] Reading input run directory
> [2024-12-12 16:40:45,754 cli_analyse INFO] selected steps: 0_topoaa,
> 1_rigidbody, 2_clustfcc, 3_contactmap
> [2024-12-12 16:40:45,754 cli_analyse INFO] Analysing step 0_topoaa
> [2024-12-12 16:40:45,755 cli_analyse WARNING] Could not execute the
> analysis for step 0_topoaa. The following error occurred 'dict' object has
> no attribute 'rel_path'
> [2024-12-12 16:40:45,755 cli_analyse INFO] Analysing step 1_rigidbody
> [2024-12-12 16:40:45,757 cli_unpack INFO] Unpacking '../1_rigidbody'
> folder
> [2024-12-12 16:40:45,758 libtimer INFO] unpacking took 0 seconds
> [2024-12-12 16:40:45,788 capri INFO] Found previous CNS step: 1_rigidbody
> [2024-12-12 16:40:46,088 capri INFO] Saved scoring weights to:
> weights_params.json
> [2024-12-12 16:40:46,088 __init__ INFO] [caprieval] No reference was
> given. Using the structure with the lowest score from previous step
> [2024-12-12 16:40:46,210 libutil INFO] Selected 5 cores to process 20
> jobs, with 16 maximum available cores.
> [2024-12-12 16:40:46,211 libparallel INFO] Using 5 cores
> [2024-12-12 16:40:46,262 libparallel WARNING] Exception in task
> execution: maximum recursion depth exceeded
> [2024-12-12 16:40:46,262 libparallel WARNING] Exception in task
> execution: maximum recursion depth exceeded
> [2024-12-12 16:40:46,263 libparallel WARNING] Exception in task
> execution: maximum recursion depth exceeded
> [2024-12-12 16:40:46,265 libparallel WARNING] Exception in task
> execution: maximum recursion depth exceeded
> [2024-12-12 16:40:46,270 libparallel WARNING] Exception in task
> execution: maximum recursion depth exceeded
> [2024-12-12 16:40:46,288 libparallel WARNING] Exception in task
> execution: maximum recursion depth exceeded
> [2024-12-12 16:40:46,290 libparallel WARNING] Exception in task
> execution: maximum recursion depth exceeded
> [2024-12-12 16:40:46,292 libparallel WARNING] Exception in task
> execution: maximum recursion depth exceeded
> [2024-12-12 16:40:46,292 libparallel WARNING] Exception in task
> execution: maximum recursion depth exceeded
> [2024-12-12 16:40:46,296 libparallel WARNING] Exception in task
> execution: maximum recursion depth exceeded
> [2024-12-12 16:40:46,313 libparallel WARNING] Exception in task
> execution: maximum recursion depth exceeded
> [2024-12-12 16:40:46,315 libparallel WARNING] Exception in task
> execution: maximum recursion depth exceeded
> [2024-12-12 16:40:46,316 libparallel WARNING] Exception in task
> execution: maximum recursion depth exceeded
> [2024-12-12 16:40:46,316 libparallel WARNING] Exception in task
> execution: maximum recursion depth exceeded
> [2024-12-12 16:40:46,321 libparallel WARNING] Exception in task
> execution: maximum recursion depth exceeded
> [2024-12-12 16:40:46,336 libparallel WARNING] Exception in task
> execution: maximum recursion depth exceeded
> [2024-12-12 16:40:46,339 libparallel WARNING] Exception in task
> execution: maximum recursion depth exceeded
> [2024-12-12 16:40:46,342 libparallel WARNING] Exception in task
> execution: maximum recursion depth exceeded
> [2024-12-12 16:40:46,342 libparallel WARNING] Exception in task
> execution: maximum recursion depth exceeded
> [2024-12-12 16:40:46,344 libparallel WARNING] Exception in task
> execution: maximum recursion depth exceeded
> [2024-12-12 16:40:46,347 libparallel INFO] 20 tasks finished
> [2024-12-12 16:40:46,348 cli_analyse WARNING] Could not execute the
> analysis for step 1_rigidbody. The following error occurred 'NoneType'
> object has no attribute 'identificator'
> [2024-12-12 16:40:46,348 cli_analyse INFO] Analysing step 2_clustfcc
> [2024-12-12 16:40:46,350 cli_unpack INFO] Unpacking '../1_rigidbody'
> folder
> [2024-12-12 16:40:46,351 libtimer INFO] unpacking took 0 seconds
> [2024-12-12 16:40:46,373 capri INFO] Found previous CNS step: 1_rigidbody
> [2024-12-12 16:40:46,646 capri INFO] Saved scoring weights to:
> weights_params.json
> [2024-12-12 16:40:46,646 __init__ INFO] [caprieval] No reference was
> given. Using the structure with the lowest score from previous step
> [2024-12-12 16:40:46,744 libutil INFO] Selected 5 cores to process 17
> jobs, with 16 maximum available cores.
> [2024-12-12 16:40:46,745 libparallel INFO] Using 5 cores
> [2024-12-12 16:40:46,792 libparallel WARNING] Exception in task
> execution: maximum recursion depth exceeded
> [2024-12-12 16:40:46,795 libparallel WARNING] Exception in task
> execution: maximum recursion depth exceeded
> [2024-12-12 16:40:46,801 libparallel WARNING] Exception in task
> execution: maximum recursion depth exceeded
> [2024-12-12 16:40:46,801 libparallel WARNING] Exception in task
> execution: maximum recursion depth exceeded
> [2024-12-12 16:40:46,804 libparallel WARNING] Exception in task
> execution: maximum recursion depth exceeded
> [2024-12-12 16:40:46,815 libparallel WARNING] Exception in task
> execution: maximum recursion depth exceeded
> [2024-12-12 16:40:46,818 libparallel WARNING] Exception in task
> execution: maximum recursion depth exceeded
> [2024-12-12 16:40:46,826 libparallel WARNING] Exception in task
> execution: maximum recursion depth exceeded
> [2024-12-12 16:40:46,830 libparallel WARNING] Exception in task
> execution: maximum recursion depth exceeded
> [2024-12-12 16:40:46,839 libparallel WARNING] Exception in task
> execution: maximum recursion depth exceeded
> [2024-12-12 16:40:46,842 libparallel WARNING] Exception in task
> execution: maximum recursion depth exceeded
> [2024-12-12 16:40:46,849 libparallel WARNING] Exception in task
> execution: maximum recursion depth exceeded
> [2024-12-12 16:40:46,854 libparallel WARNING] Exception in task
> execution: maximum recursion depth exceeded
> [2024-12-12 16:40:46,861 libparallel WARNING] Exception in task
> execution: maximum recursion depth exceeded
> [2024-12-12 16:40:46,865 libparallel WARNING] Exception in task
> execution: maximum recursion depth exceeded
> [2024-12-12 16:40:46,870 libparallel WARNING] Exception in task
> execution: maximum recursion depth exceeded
> [2024-12-12 16:40:46,879 libparallel WARNING] Exception in task
> execution: maximum recursion depth exceeded
> [2024-12-12 16:40:46,882 libparallel INFO] 17 tasks finished
> [2024-12-12 16:40:46,883 cli_analyse WARNING] Could not execute the
> analysis for step 2_clustfcc. The following error occurred 'NoneType'
> object has no attribute 'identificator'
> [2024-12-12 16:40:46,883 cli_analyse INFO] Analysing step 3_contactmap
> [2024-12-12 16:40:46,885 cli_unpack INFO] Unpacking '../1_rigidbody'
> folder
> [2024-12-12 16:40:46,886 libtimer INFO] unpacking took 0 seconds
> [2024-12-12 16:40:46,907 capri INFO] Found previous CNS step: 1_rigidbody
> [2024-12-12 16:40:47,177 capri INFO] Saved scoring weights to:
> weights_params.json
> [2024-12-12 16:40:47,177 __init__ INFO] [caprieval] No reference was
> given. Using the structure with the lowest score from previous step
> [2024-12-12 16:40:47,272 libutil INFO] Selected 5 cores to process 17
> jobs, with 16 maximum available cores.
> [2024-12-12 16:40:47,273 libparallel INFO] Using 5 cores
> [2024-12-12 16:40:47,314 libparallel WARNING] Exception in task
> execution: maximum recursion depth exceeded
> [2024-12-12 16:40:47,319 libparallel WARNING] Exception in task
> execution: maximum recursion depth exceeded
> [2024-12-12 16:40:47,323 libparallel WARNING] Exception in task
> execution: maximum recursion depth exceeded
> [2024-12-12 16:40:47,326 libparallel WARNING] Exception in task
> execution: maximum recursion depth exceeded
> [2024-12-12 16:40:47,329 libparallel WARNING] Exception in task
> execution: maximum recursion depth exceeded
> [2024-12-12 16:40:47,339 libparallel WARNING] Exception in task
> execution: maximum recursion depth exceeded
> [2024-12-12 16:40:47,342 libparallel WARNING] Exception in task
> execution: maximum recursion depth exceeded
> [2024-12-12 16:40:47,346 libparallel WARNING] Exception in task
> execution: maximum recursion depth exceeded
> [2024-12-12 16:40:47,351 libparallel WARNING] Exception in task
> execution: maximum recursion depth exceeded
> [2024-12-12 16:40:47,362 libparallel WARNING] Exception in task
> execution: maximum recursion depth exceeded
> [2024-12-12 16:40:47,365 libparallel WARNING] Exception in task
> execution: maximum recursion depth exceeded
> [2024-12-12 16:40:47,368 libparallel WARNING] Exception in task
> execution: maximum recursion depth exceeded
> [2024-12-12 16:40:47,374 libparallel WARNING] Exception in task
> execution: maximum recursion depth exceeded
> [2024-12-12 16:40:47,384 libparallel WARNING] Exception in task
> execution: maximum recursion depth exceeded
> [2024-12-12 16:40:47,387 libparallel WARNING] Exception in task
> execution: maximum recursion depth exceeded
> [2024-12-12 16:40:47,391 libparallel WARNING] Exception in task
> execution: maximum recursion depth exceeded
> [2024-12-12 16:40:47,397 libparallel WARNING] Exception in task
> execution: maximum recursion depth exceeded
> [2024-12-12 16:40:47,401 libparallel INFO] 17 tasks finished
> [2024-12-12 16:40:47,401 cli_analyse WARNING] Could not execute the
> analysis for step 3_contactmap. The following error occurred 'NoneType'
> object has no attribute 'identificator'
> [2024-12-12 16:40:47,401 cli_analyse INFO] cancelling unsuccesful
> analysis folders
> [2024-12-12 16:40:47,402 cli_traceback INFO] Running haddock3-traceback
> on ./
> [2024-12-12 16:40:47,402 cli_traceback INFO] Reading input run directory
> [2024-12-12 16:40:47,402 cli_traceback INFO] All_steps: 0_topoaa,
> 1_rigidbody, 2_clustfcc, 3_contactmap
> [2024-12-12 16:40:47,403 cli_traceback INFO] Modules not to be analysed:
> 0_topoaa, 2_clustfcc, 3_contactmap
> [2024-12-12 16:40:47,403 cli_traceback INFO] Steps to trace back:
> 1_rigidbody
> [2024-12-12 16:40:47,403 cli_traceback INFO] Created directory:
> /home/root777/haddock3/examples/analysis/test_contmap/traceback
> [2024-12-12 16:40:47,403 cli_traceback INFO] Tracing back step 1_rigidbody
> [2024-12-12 16:40:47,408 libworkflow WARNING] Error running traceback:
> Cannot convert numpy.ndarray to numpy.ndarray
> [2024-12-12 16:40:47,408 clean_steps INFO] Cleaning output for '0_topoaa'
> using 5 cores.
> [2024-12-12 16:40:47,573 libtimer INFO] cleaning output files took 0
> seconds
> [2024-12-12 16:40:47,573 clean_steps INFO] Cleaning output for
> '1_rigidbody' using 5 cores.
> [2024-12-12 16:40:47,988 libtimer INFO] cleaning output files took 0
> seconds
> [2024-12-12 16:40:47,989 clean_steps INFO] Cleaning output for
> '2_clustfcc' using 5 cores.
> [2024-12-12 16:40:48,023 libtimer INFO] cleaning output files took 0
> seconds
> [2024-12-12 16:40:48,023 clean_steps INFO] Cleaning output for
> '3_contactmap' using 5 cores.
> [2024-12-12 16:40:48,034 libtimer INFO] cleaning output files took 0
> seconds
> [2024-12-12 16:40:48,035 cli INFO] This HADDOCK3 run took: 54 seconds
> [2024-12-12 16:40:48,035 greetings INFO] Your feedback matters in
> Haddock3! Share your experience and help us grow:
> [2024-12-12 16:40:48,035 greetings INFO] GitHub issues:
> https://github.com/haddocking/haddock3/issues
> [2024-12-12 16:40:48,035 greetings INFO] BioExcel feedback:
> https://www.bonvinlab.org/feedback
> [2024-12-12 16:40:48,035 greetings INFO] BioExcel forum:
> https://ask.bioexcel.eu/c/haddock/6
> [2024-12-12 16:40:48,035 cli INFO] Finished at 12/12/2024 16:40:48. Tot
> ziens! Dovidenia! 再见!
>
>
> On Thu, 12 Dec 2024 at 14:02, Alexandre Bonvin ***@***.***>
> wrote:
>
>> Results are only kept for two
>> weeks…================================= Prof. A.M.J.J. Bonvin | Faculty of
>> Science Utrecht University | ***@***.*** | T: +31 30
>> 2533859 =================================On 11 Dec 2024, at 18:13,
>> Harshilwalia777 ***@***.***> wrote:
>> how to resolve it, pls help
>>
>> —Reply to this email directly, view it on GitHub, or unsubscribe.You are
>> receiving this because you are subscribed to this thread.Message ID:
>> ***@***.***>
>>
>> —
>> Reply to this email directly, view it on GitHub
>> <#1181 (comment)>,
>> or unsubscribe
>> <https://github.com/notifications/unsubscribe-auth/A6NCZIHPLIM6XTEIRPOMCFL2FFC3PAVCNFSM6AAAAABTN6YFMWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDKMZYGE4DKMBWHA>
>> .
>> You are receiving this because you authored the thread.Message ID:
>> ***@***.***>
>>
>
|
|
here is also the installation output:
Processing /home/root777/haddock3
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... done
Requirement already satisfied: pdb-tools>=2.5.0 in
/home/root777/anaconda3/envs/haddock/lib/python3.12/site-packages (from
haddock3==2024.10.0b7) (2.5.0)
Requirement already satisfied: biopython==1.* in
/home/root777/anaconda3/envs/haddock/lib/python3.12/site-packages (from
haddock3==2024.10.0b7) (1.84)
Requirement already satisfied: jsonpickle>=2.1.0 in
/home/root777/anaconda3/envs/haddock/lib/python3.12/site-packages (from
haddock3==2024.10.0b7) (4.0.0)
Requirement already satisfied: numpy==2.* in
/home/root777/anaconda3/envs/haddock/lib/python3.12/site-packages (from
haddock3==2024.10.0b7) (2.2.0)
Requirement already satisfied: pyyaml>=6.0 in
/home/root777/anaconda3/envs/haddock/lib/python3.12/site-packages (from
haddock3==2024.10.0b7) (6.0.2)
Requirement already satisfied: scipy>=1.10.0 in
/home/root777/anaconda3/envs/haddock/lib/python3.12/site-packages (from
haddock3==2024.10.0b7) (1.13.1)
Requirement already satisfied: toml>=0.10.2 in
/home/root777/anaconda3/envs/haddock/lib/python3.12/site-packages (from
haddock3==2024.10.0b7) (0.10.2)
Requirement already satisfied: pandas==2.* in
/home/root777/anaconda3/envs/haddock/lib/python3.12/site-packages (from
haddock3==2024.10.0b7) (2.2.3)
Requirement already satisfied: plotly==5.24.1 in
/home/root777/anaconda3/envs/haddock/lib/python3.12/site-packages (from
haddock3==2024.10.0b7) (5.24.1)
Requirement already satisfied: freesasa>=2.2.1 in
/home/root777/anaconda3/envs/haddock/lib/python3.12/site-packages (from
haddock3==2024.10.0b7) (2.2.1)
Requirement already satisfied: python-dateutil>=2.8.2 in
/home/root777/anaconda3/envs/haddock/lib/python3.12/site-packages (from
pandas==2.*->haddock3==2024.10.0b7) (2.9.0.post0)
Requirement already satisfied: pytz>=2020.1 in
/home/root777/anaconda3/envs/haddock/lib/python3.12/site-packages (from
pandas==2.*->haddock3==2024.10.0b7) (2024.2)
Requirement already satisfied: tzdata>=2022.7 in
/home/root777/anaconda3/envs/haddock/lib/python3.12/site-packages (from
pandas==2.*->haddock3==2024.10.0b7) (2024.2)
Requirement already satisfied: tenacity>=6.2.0 in
/home/root777/anaconda3/envs/haddock/lib/python3.12/site-packages (from
plotly==5.24.1->haddock3==2024.10.0b7) (9.0.0)
Requirement already satisfied: packaging in
/home/root777/anaconda3/envs/haddock/lib/python3.12/site-packages (from
plotly==5.24.1->haddock3==2024.10.0b7) (24.2)
Requirement already satisfied: six>=1.5 in
/home/root777/anaconda3/envs/haddock/lib/python3.12/site-packages (from
python-dateutil>=2.8.2->pandas==2.*->haddock3==2024.10.0b7) (1.17.0)
Building wheels for collected packages: haddock3
Building wheel for haddock3 (pyproject.toml) ... done
Created wheel for haddock3:
filename=haddock3-2024.10.0b7-cp312-cp312-linux_x86_64.whl size=3879011
sha256=8af440b991421fad83e657b904767885eeea0e8e5a5baf0df1c8ab4d0c3c079c
Stored in directory:
/tmp/pip-ephem-wheel-cache-jabu2i_p/wheels/f3/33/7f/c5181cd99a02e0daf8ffbdb8a28bb01fa3edb5c558419b7bb4
Successfully built haddock3
Installing collected packages: haddock3
Attempting uninstall: haddock3
Found existing installation: haddock3 2024.10.0b7
Uninstalling haddock3-2024.10.0b7:
Successfully uninstalled haddock3-2024.10.0b7
Successfully installed haddock3-2024.10.0b7
On Thu, 12 Dec 2024 at 16:43, Harshil Walia ***@***.***>
wrote:
… run analysis file 'contactmap.cfg' for checking haddock3
On Thu, 12 Dec 2024 at 16:42, Harshil Walia ***@***.***>
wrote:
> same result after reinstalling it.
>
>
> On Thu, 12 Dec 2024 at 16:41, Harshil Walia ***@***.***>
> wrote:
>
>> [2024-12-12 16:40:45,738 contmap INFO] Generated report file:
>> ContactMapReport.html
>> [2024-12-12 16:40:45,743 __init__ INFO] Module [contactmap] finished.
>> [2024-12-12 16:40:45,743 __init__ INFO] [contactmap] took 0 seconds
>> [2024-12-12 16:40:45,743 cli_analyse INFO] Running haddock3-analyse on
>> ./, modules [], with top_cluster = 10
>> [2024-12-12 16:40:45,754 cli_analyse INFO] Created directory:
>> /home/root777/haddock3/examples/analysis/test_contmap/analysis
>> [2024-12-12 16:40:45,754 cli_analyse INFO] Reading input run directory
>> [2024-12-12 16:40:45,754 cli_analyse INFO] selected steps: 0_topoaa,
>> 1_rigidbody, 2_clustfcc, 3_contactmap
>> [2024-12-12 16:40:45,754 cli_analyse INFO] Analysing step 0_topoaa
>> [2024-12-12 16:40:45,755 cli_analyse WARNING] Could not execute the
>> analysis for step 0_topoaa. The following error occurred 'dict' object has
>> no attribute 'rel_path'
>> [2024-12-12 16:40:45,755 cli_analyse INFO] Analysing step 1_rigidbody
>> [2024-12-12 16:40:45,757 cli_unpack INFO] Unpacking '../1_rigidbody'
>> folder
>> [2024-12-12 16:40:45,758 libtimer INFO] unpacking took 0 seconds
>> [2024-12-12 16:40:45,788 capri INFO] Found previous CNS step: 1_rigidbody
>> [2024-12-12 16:40:46,088 capri INFO] Saved scoring weights to:
>> weights_params.json
>> [2024-12-12 16:40:46,088 __init__ INFO] [caprieval] No reference was
>> given. Using the structure with the lowest score from previous step
>> [2024-12-12 16:40:46,210 libutil INFO] Selected 5 cores to process 20
>> jobs, with 16 maximum available cores.
>> [2024-12-12 16:40:46,211 libparallel INFO] Using 5 cores
>> [2024-12-12 16:40:46,262 libparallel WARNING] Exception in task
>> execution: maximum recursion depth exceeded
>> [2024-12-12 16:40:46,262 libparallel WARNING] Exception in task
>> execution: maximum recursion depth exceeded
>> [2024-12-12 16:40:46,263 libparallel WARNING] Exception in task
>> execution: maximum recursion depth exceeded
>> [2024-12-12 16:40:46,265 libparallel WARNING] Exception in task
>> execution: maximum recursion depth exceeded
>> [2024-12-12 16:40:46,270 libparallel WARNING] Exception in task
>> execution: maximum recursion depth exceeded
>> [2024-12-12 16:40:46,288 libparallel WARNING] Exception in task
>> execution: maximum recursion depth exceeded
>> [2024-12-12 16:40:46,290 libparallel WARNING] Exception in task
>> execution: maximum recursion depth exceeded
>> [2024-12-12 16:40:46,292 libparallel WARNING] Exception in task
>> execution: maximum recursion depth exceeded
>> [2024-12-12 16:40:46,292 libparallel WARNING] Exception in task
>> execution: maximum recursion depth exceeded
>> [2024-12-12 16:40:46,296 libparallel WARNING] Exception in task
>> execution: maximum recursion depth exceeded
>> [2024-12-12 16:40:46,313 libparallel WARNING] Exception in task
>> execution: maximum recursion depth exceeded
>> [2024-12-12 16:40:46,315 libparallel WARNING] Exception in task
>> execution: maximum recursion depth exceeded
>> [2024-12-12 16:40:46,316 libparallel WARNING] Exception in task
>> execution: maximum recursion depth exceeded
>> [2024-12-12 16:40:46,316 libparallel WARNING] Exception in task
>> execution: maximum recursion depth exceeded
>> [2024-12-12 16:40:46,321 libparallel WARNING] Exception in task
>> execution: maximum recursion depth exceeded
>> [2024-12-12 16:40:46,336 libparallel WARNING] Exception in task
>> execution: maximum recursion depth exceeded
>> [2024-12-12 16:40:46,339 libparallel WARNING] Exception in task
>> execution: maximum recursion depth exceeded
>> [2024-12-12 16:40:46,342 libparallel WARNING] Exception in task
>> execution: maximum recursion depth exceeded
>> [2024-12-12 16:40:46,342 libparallel WARNING] Exception in task
>> execution: maximum recursion depth exceeded
>> [2024-12-12 16:40:46,344 libparallel WARNING] Exception in task
>> execution: maximum recursion depth exceeded
>> [2024-12-12 16:40:46,347 libparallel INFO] 20 tasks finished
>> [2024-12-12 16:40:46,348 cli_analyse WARNING] Could not execute the
>> analysis for step 1_rigidbody. The following error occurred 'NoneType'
>> object has no attribute 'identificator'
>> [2024-12-12 16:40:46,348 cli_analyse INFO] Analysing step 2_clustfcc
>> [2024-12-12 16:40:46,350 cli_unpack INFO] Unpacking '../1_rigidbody'
>> folder
>> [2024-12-12 16:40:46,351 libtimer INFO] unpacking took 0 seconds
>> [2024-12-12 16:40:46,373 capri INFO] Found previous CNS step: 1_rigidbody
>> [2024-12-12 16:40:46,646 capri INFO] Saved scoring weights to:
>> weights_params.json
>> [2024-12-12 16:40:46,646 __init__ INFO] [caprieval] No reference was
>> given. Using the structure with the lowest score from previous step
>> [2024-12-12 16:40:46,744 libutil INFO] Selected 5 cores to process 17
>> jobs, with 16 maximum available cores.
>> [2024-12-12 16:40:46,745 libparallel INFO] Using 5 cores
>> [2024-12-12 16:40:46,792 libparallel WARNING] Exception in task
>> execution: maximum recursion depth exceeded
>> [2024-12-12 16:40:46,795 libparallel WARNING] Exception in task
>> execution: maximum recursion depth exceeded
>> [2024-12-12 16:40:46,801 libparallel WARNING] Exception in task
>> execution: maximum recursion depth exceeded
>> [2024-12-12 16:40:46,801 libparallel WARNING] Exception in task
>> execution: maximum recursion depth exceeded
>> [2024-12-12 16:40:46,804 libparallel WARNING] Exception in task
>> execution: maximum recursion depth exceeded
>> [2024-12-12 16:40:46,815 libparallel WARNING] Exception in task
>> execution: maximum recursion depth exceeded
>> [2024-12-12 16:40:46,818 libparallel WARNING] Exception in task
>> execution: maximum recursion depth exceeded
>> [2024-12-12 16:40:46,826 libparallel WARNING] Exception in task
>> execution: maximum recursion depth exceeded
>> [2024-12-12 16:40:46,830 libparallel WARNING] Exception in task
>> execution: maximum recursion depth exceeded
>> [2024-12-12 16:40:46,839 libparallel WARNING] Exception in task
>> execution: maximum recursion depth exceeded
>> [2024-12-12 16:40:46,842 libparallel WARNING] Exception in task
>> execution: maximum recursion depth exceeded
>> [2024-12-12 16:40:46,849 libparallel WARNING] Exception in task
>> execution: maximum recursion depth exceeded
>> [2024-12-12 16:40:46,854 libparallel WARNING] Exception in task
>> execution: maximum recursion depth exceeded
>> [2024-12-12 16:40:46,861 libparallel WARNING] Exception in task
>> execution: maximum recursion depth exceeded
>> [2024-12-12 16:40:46,865 libparallel WARNING] Exception in task
>> execution: maximum recursion depth exceeded
>> [2024-12-12 16:40:46,870 libparallel WARNING] Exception in task
>> execution: maximum recursion depth exceeded
>> [2024-12-12 16:40:46,879 libparallel WARNING] Exception in task
>> execution: maximum recursion depth exceeded
>> [2024-12-12 16:40:46,882 libparallel INFO] 17 tasks finished
>> [2024-12-12 16:40:46,883 cli_analyse WARNING] Could not execute the
>> analysis for step 2_clustfcc. The following error occurred 'NoneType'
>> object has no attribute 'identificator'
>> [2024-12-12 16:40:46,883 cli_analyse INFO] Analysing step 3_contactmap
>> [2024-12-12 16:40:46,885 cli_unpack INFO] Unpacking '../1_rigidbody'
>> folder
>> [2024-12-12 16:40:46,886 libtimer INFO] unpacking took 0 seconds
>> [2024-12-12 16:40:46,907 capri INFO] Found previous CNS step: 1_rigidbody
>> [2024-12-12 16:40:47,177 capri INFO] Saved scoring weights to:
>> weights_params.json
>> [2024-12-12 16:40:47,177 __init__ INFO] [caprieval] No reference was
>> given. Using the structure with the lowest score from previous step
>> [2024-12-12 16:40:47,272 libutil INFO] Selected 5 cores to process 17
>> jobs, with 16 maximum available cores.
>> [2024-12-12 16:40:47,273 libparallel INFO] Using 5 cores
>> [2024-12-12 16:40:47,314 libparallel WARNING] Exception in task
>> execution: maximum recursion depth exceeded
>> [2024-12-12 16:40:47,319 libparallel WARNING] Exception in task
>> execution: maximum recursion depth exceeded
>> [2024-12-12 16:40:47,323 libparallel WARNING] Exception in task
>> execution: maximum recursion depth exceeded
>> [2024-12-12 16:40:47,326 libparallel WARNING] Exception in task
>> execution: maximum recursion depth exceeded
>> [2024-12-12 16:40:47,329 libparallel WARNING] Exception in task
>> execution: maximum recursion depth exceeded
>> [2024-12-12 16:40:47,339 libparallel WARNING] Exception in task
>> execution: maximum recursion depth exceeded
>> [2024-12-12 16:40:47,342 libparallel WARNING] Exception in task
>> execution: maximum recursion depth exceeded
>> [2024-12-12 16:40:47,346 libparallel WARNING] Exception in task
>> execution: maximum recursion depth exceeded
>> [2024-12-12 16:40:47,351 libparallel WARNING] Exception in task
>> execution: maximum recursion depth exceeded
>> [2024-12-12 16:40:47,362 libparallel WARNING] Exception in task
>> execution: maximum recursion depth exceeded
>> [2024-12-12 16:40:47,365 libparallel WARNING] Exception in task
>> execution: maximum recursion depth exceeded
>> [2024-12-12 16:40:47,368 libparallel WARNING] Exception in task
>> execution: maximum recursion depth exceeded
>> [2024-12-12 16:40:47,374 libparallel WARNING] Exception in task
>> execution: maximum recursion depth exceeded
>> [2024-12-12 16:40:47,384 libparallel WARNING] Exception in task
>> execution: maximum recursion depth exceeded
>> [2024-12-12 16:40:47,387 libparallel WARNING] Exception in task
>> execution: maximum recursion depth exceeded
>> [2024-12-12 16:40:47,391 libparallel WARNING] Exception in task
>> execution: maximum recursion depth exceeded
>> [2024-12-12 16:40:47,397 libparallel WARNING] Exception in task
>> execution: maximum recursion depth exceeded
>> [2024-12-12 16:40:47,401 libparallel INFO] 17 tasks finished
>> [2024-12-12 16:40:47,401 cli_analyse WARNING] Could not execute the
>> analysis for step 3_contactmap. The following error occurred 'NoneType'
>> object has no attribute 'identificator'
>> [2024-12-12 16:40:47,401 cli_analyse INFO] cancelling unsuccesful
>> analysis folders
>> [2024-12-12 16:40:47,402 cli_traceback INFO] Running haddock3-traceback
>> on ./
>> [2024-12-12 16:40:47,402 cli_traceback INFO] Reading input run directory
>> [2024-12-12 16:40:47,402 cli_traceback INFO] All_steps: 0_topoaa,
>> 1_rigidbody, 2_clustfcc, 3_contactmap
>> [2024-12-12 16:40:47,403 cli_traceback INFO] Modules not to be analysed:
>> 0_topoaa, 2_clustfcc, 3_contactmap
>> [2024-12-12 16:40:47,403 cli_traceback INFO] Steps to trace back:
>> 1_rigidbody
>> [2024-12-12 16:40:47,403 cli_traceback INFO] Created directory:
>> /home/root777/haddock3/examples/analysis/test_contmap/traceback
>> [2024-12-12 16:40:47,403 cli_traceback INFO] Tracing back step
>> 1_rigidbody
>> [2024-12-12 16:40:47,408 libworkflow WARNING] Error running traceback:
>> Cannot convert numpy.ndarray to numpy.ndarray
>> [2024-12-12 16:40:47,408 clean_steps INFO] Cleaning output for
>> '0_topoaa' using 5 cores.
>> [2024-12-12 16:40:47,573 libtimer INFO] cleaning output files took 0
>> seconds
>> [2024-12-12 16:40:47,573 clean_steps INFO] Cleaning output for
>> '1_rigidbody' using 5 cores.
>> [2024-12-12 16:40:47,988 libtimer INFO] cleaning output files took 0
>> seconds
>> [2024-12-12 16:40:47,989 clean_steps INFO] Cleaning output for
>> '2_clustfcc' using 5 cores.
>> [2024-12-12 16:40:48,023 libtimer INFO] cleaning output files took 0
>> seconds
>> [2024-12-12 16:40:48,023 clean_steps INFO] Cleaning output for
>> '3_contactmap' using 5 cores.
>> [2024-12-12 16:40:48,034 libtimer INFO] cleaning output files took 0
>> seconds
>> [2024-12-12 16:40:48,035 cli INFO] This HADDOCK3 run took: 54 seconds
>> [2024-12-12 16:40:48,035 greetings INFO] Your feedback matters in
>> Haddock3! Share your experience and help us grow:
>> [2024-12-12 16:40:48,035 greetings INFO] GitHub issues:
>> https://github.com/haddocking/haddock3/issues
>> [2024-12-12 16:40:48,035 greetings INFO] BioExcel feedback:
>> https://www.bonvinlab.org/feedback
>> [2024-12-12 16:40:48,035 greetings INFO] BioExcel forum:
>> https://ask.bioexcel.eu/c/haddock/6
>> [2024-12-12 16:40:48,035 cli INFO] Finished at 12/12/2024 16:40:48. Tot
>> ziens! Dovidenia! 再见!
>>
>>
>> On Thu, 12 Dec 2024 at 14:02, Alexandre Bonvin ***@***.***>
>> wrote:
>>
>>> Results are only kept for two
>>> weeks…================================= Prof. A.M.J.J. Bonvin | Faculty of
>>> Science Utrecht University | ***@***.*** | T: +31 30
>>> 2533859 =================================On 11 Dec 2024, at 18:13,
>>> Harshilwalia777 ***@***.***> wrote:
>>> how to resolve it, pls help
>>>
>>> —Reply to this email directly, view it on GitHub, or unsubscribe.You
>>> are receiving this because you are subscribed to this thread.Message ID:
>>> ***@***.***>
>>>
>>> —
>>> Reply to this email directly, view it on GitHub
>>> <#1181 (comment)>,
>>> or unsubscribe
>>> <https://github.com/notifications/unsubscribe-auth/A6NCZIHPLIM6XTEIRPOMCFL2FFC3PAVCNFSM6AAAAABTN6YFMWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDKMZYGE4DKMBWHA>
>>> .
>>> You are receiving this because you authored the thread.Message ID:
>>> ***@***.***>
>>>
>>
|
|
And you are running the default test example, no modifications?
On what hardware / operating system are you running?
We can not reproduce this problem.
|
|
default test examples which executed on local computer
…On Thu, 12 Dec 2024 at 16:57, Alexandre Bonvin ***@***.***> wrote:
And you are running the default test example, no modifications?
On what hardware / operating system are you running?
We can not reproduce this problem.
—
Reply to this email directly, view it on GitHub
<#1181 (comment)>,
or unsubscribe
<https://github.com/notifications/unsubscribe-auth/A6NCZIBN2DK4ZWW5W45ZI7D2FFXITAVCNFSM6AAAAABTN6YFMWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDKMZYGYZDEMJUHA>
.
You are receiving this because you were mentioned.Message ID:
***@***.***>
|
|
OS Name Microsoft Windows 11 Home
Version 10.0.22631 Build 22631
Other OS Description Not Available
OS Manufacturer Microsoft Corporation
System Name LAPTOP-CFDC89M7
System Manufacturer Acer
System Model Aspire A515-57
System Type x64-based PC
System SKU 0000000000000000
Processor 12th Gen Intel(R) Core(TM) i7-12650H, 2300 Mhz, 10 Core(s), 16
Logical Processor(s)
BIOS Version/Date Insyde Corp. V1.22, 5/31/2023
SMBIOS Version 3.3
Embedded Controller Version 1.15
BIOS Mode UEFI
BaseBoard Manufacturer ADL
BaseBoard Product Ganymede_ADU
BaseBoard Version V1.22
Platform Role Mobile
Secure Boot State On
PCR7 Configuration Elevation Required to View
Windows Directory C:\Windows
System Directory C:\Windows\system32
Boot Device \Device\HarddiskVolume1
Locale United States
Hardware Abstraction Layer Version = "10.0.22621.2506"
User Name LAPTOP-CFDC89M7\harsh
Time Zone India Standard Time
Installed Physical Memory (RAM) 32.0 GB
Total Physical Memory 31.7 GB
Available Physical Memory 18.2 GB
Total Virtual Memory 33.7 GB
Available Virtual Memory 17.3 GB
Page File Space 2.00 GB
Page File C:\pagefile.sys
Kernel DMA Protection On
Virtualization-based security Running
Virtualization-based security Required Security Properties
Virtualization-based security Available Security Properties Base
Virtualization Support, Secure Boot, DMA Protection, UEFI Code Readonly,
SMM Security Mitigations 1.0, Mode Based Execution Control, APIC
Virtualization
Virtualization-based security Services Configured Hypervisor enforced Code
Integrity
Virtualization-based security Services Running Hypervisor enforced Code
Integrity
Windows Defender Application Control policy Enforced
Windows Defender Application Control user mode policy Off
Device Encryption Support Elevation Required to View
A hypervisor has been detected. Features required for Hyper-V will not be
displayed.
On Thu, 12 Dec 2024 at 16:58, Harshil Walia ***@***.***>
wrote:
… default test examples which executed on local computer
On Thu, 12 Dec 2024 at 16:57, Alexandre Bonvin ***@***.***>
wrote:
> And you are running the default test example, no modifications?
>
> On what hardware / operating system are you running?
>
> We can not reproduce this problem.
>
> —
> Reply to this email directly, view it on GitHub
> <#1181 (comment)>,
> or unsubscribe
> <https://github.com/notifications/unsubscribe-auth/A6NCZIBN2DK4ZWW5W45ZI7D2FFXITAVCNFSM6AAAAABTN6YFMWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDKMZYGYZDEMJUHA>
> .
> You are receiving this because you were mentioned.Message ID:
> ***@***.***>
>
|
|
using wsl ubuntu
On Thu, 12 Dec 2024 at 16:59, Harshil Walia ***@***.***>
wrote:
… OS Name Microsoft Windows 11 Home
Version 10.0.22631 Build 22631
Other OS Description Not Available
OS Manufacturer Microsoft Corporation
System Name LAPTOP-CFDC89M7
System Manufacturer Acer
System Model Aspire A515-57
System Type x64-based PC
System SKU 0000000000000000
Processor 12th Gen Intel(R) Core(TM) i7-12650H, 2300 Mhz, 10 Core(s), 16
Logical Processor(s)
BIOS Version/Date Insyde Corp. V1.22, 5/31/2023
SMBIOS Version 3.3
Embedded Controller Version 1.15
BIOS Mode UEFI
BaseBoard Manufacturer ADL
BaseBoard Product Ganymede_ADU
BaseBoard Version V1.22
Platform Role Mobile
Secure Boot State On
PCR7 Configuration Elevation Required to View
Windows Directory C:\Windows
System Directory C:\Windows\system32
Boot Device \Device\HarddiskVolume1
Locale United States
Hardware Abstraction Layer Version = "10.0.22621.2506"
User Name LAPTOP-CFDC89M7\harsh
Time Zone India Standard Time
Installed Physical Memory (RAM) 32.0 GB
Total Physical Memory 31.7 GB
Available Physical Memory 18.2 GB
Total Virtual Memory 33.7 GB
Available Virtual Memory 17.3 GB
Page File Space 2.00 GB
Page File C:\pagefile.sys
Kernel DMA Protection On
Virtualization-based security Running
Virtualization-based security Required Security Properties
Virtualization-based security Available Security Properties Base
Virtualization Support, Secure Boot, DMA Protection, UEFI Code Readonly,
SMM Security Mitigations 1.0, Mode Based Execution Control, APIC
Virtualization
Virtualization-based security Services Configured Hypervisor enforced Code
Integrity
Virtualization-based security Services Running Hypervisor enforced Code
Integrity
Windows Defender Application Control policy Enforced
Windows Defender Application Control user mode policy Off
Device Encryption Support Elevation Required to View
A hypervisor has been detected. Features required for Hyper-V will not be
displayed.
On Thu, 12 Dec 2024 at 16:58, Harshil Walia ***@***.***>
wrote:
> default test examples which executed on local computer
>
> On Thu, 12 Dec 2024 at 16:57, Alexandre Bonvin ***@***.***>
> wrote:
>
>> And you are running the default test example, no modifications?
>>
>> On what hardware / operating system are you running?
>>
>> We can not reproduce this problem.
>>
>> —
>> Reply to this email directly, view it on GitHub
>> <#1181 (comment)>,
>> or unsubscribe
>> <https://github.com/notifications/unsubscribe-auth/A6NCZIBN2DK4ZWW5W45ZI7D2FFXITAVCNFSM6AAAAABTN6YFMWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDKMZYGYZDEMJUHA>
>> .
>> You are receiving this because you were mentioned.Message ID:
>> ***@***.***>
>>
>
|
|
ubuntu version is up to date
On Thu, 12 Dec 2024 at 16:59, Harshil Walia ***@***.***>
wrote:
… using wsl ubuntu
On Thu, 12 Dec 2024 at 16:59, Harshil Walia ***@***.***>
wrote:
> OS Name Microsoft Windows 11 Home
> Version 10.0.22631 Build 22631
> Other OS Description Not Available
> OS Manufacturer Microsoft Corporation
> System Name LAPTOP-CFDC89M7
> System Manufacturer Acer
> System Model Aspire A515-57
> System Type x64-based PC
> System SKU 0000000000000000
> Processor 12th Gen Intel(R) Core(TM) i7-12650H, 2300 Mhz, 10 Core(s), 16
> Logical Processor(s)
> BIOS Version/Date Insyde Corp. V1.22, 5/31/2023
> SMBIOS Version 3.3
> Embedded Controller Version 1.15
> BIOS Mode UEFI
> BaseBoard Manufacturer ADL
> BaseBoard Product Ganymede_ADU
> BaseBoard Version V1.22
> Platform Role Mobile
> Secure Boot State On
> PCR7 Configuration Elevation Required to View
> Windows Directory C:\Windows
> System Directory C:\Windows\system32
> Boot Device \Device\HarddiskVolume1
> Locale United States
> Hardware Abstraction Layer Version = "10.0.22621.2506"
> User Name LAPTOP-CFDC89M7\harsh
> Time Zone India Standard Time
> Installed Physical Memory (RAM) 32.0 GB
> Total Physical Memory 31.7 GB
> Available Physical Memory 18.2 GB
> Total Virtual Memory 33.7 GB
> Available Virtual Memory 17.3 GB
> Page File Space 2.00 GB
> Page File C:\pagefile.sys
> Kernel DMA Protection On
> Virtualization-based security Running
> Virtualization-based security Required Security Properties
> Virtualization-based security Available Security Properties Base
> Virtualization Support, Secure Boot, DMA Protection, UEFI Code Readonly,
> SMM Security Mitigations 1.0, Mode Based Execution Control, APIC
> Virtualization
> Virtualization-based security Services Configured Hypervisor enforced
> Code Integrity
> Virtualization-based security Services Running Hypervisor enforced Code
> Integrity
> Windows Defender Application Control policy Enforced
> Windows Defender Application Control user mode policy Off
> Device Encryption Support Elevation Required to View
> A hypervisor has been detected. Features required for Hyper-V will not be
> displayed.
>
> On Thu, 12 Dec 2024 at 16:58, Harshil Walia ***@***.***>
> wrote:
>
>> default test examples which executed on local computer
>>
>> On Thu, 12 Dec 2024 at 16:57, Alexandre Bonvin ***@***.***>
>> wrote:
>>
>>> And you are running the default test example, no modifications?
>>>
>>> On what hardware / operating system are you running?
>>>
>>> We can not reproduce this problem.
>>>
>>> —
>>> Reply to this email directly, view it on GitHub
>>> <#1181 (comment)>,
>>> or unsubscribe
>>> <https://github.com/notifications/unsubscribe-auth/A6NCZIBN2DK4ZWW5W45ZI7D2FFXITAVCNFSM6AAAAABTN6YFMWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDKMZYGYZDEMJUHA>
>>> .
>>> You are receiving this because you were mentioned.Message ID:
>>> ***@***.***>
>>>
>>
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Python 3.12.2 | packaged by conda-forge | (main, Feb 16 2024, 20:50:58) [GCC 12.3.0]
[2024-12-11 22:37:53,952 libworkflow INFO] Reading instructions step 0_topoaa
[2024-12-11 22:37:53,952 libworkflow INFO] Reading instructions step 1_rigidbody
[2024-12-11 22:37:53,953 libworkflow INFO] Reading instructions step 2_caprieval
[2024-12-11 22:37:53,953 libworkflow INFO] Reading instructions step 3_seletop
[2024-12-11 22:37:53,953 libworkflow INFO] Reading instructions step 4_caprieval
[2024-12-11 22:37:53,953 libworkflow INFO] Reading instructions step 5_flexref
[2024-12-11 22:37:53,953 libworkflow INFO] Reading instructions step 6_caprieval
[2024-12-11 22:37:53,953 libworkflow INFO] Reading instructions step 7_emref
[2024-12-11 22:37:53,953 libworkflow INFO] Reading instructions step 8_caprieval
[2024-12-11 22:37:53,954 libworkflow INFO] Reading instructions step 9_clustfcc
[2024-12-11 22:37:53,954 libworkflow INFO] Reading instructions step 10_seletopclusts
[2024-12-11 22:37:53,954 libworkflow INFO] Reading instructions step 11_caprieval
[2024-12-11 22:37:53,968 base_cns_module INFO] Running [topoaa] module
[2024-12-11 22:37:53,968 init INFO] [topoaa] Molecule 1: cro.pdb
[2024-12-11 22:37:53,969 init INFO] [topoaa] Sanitizing molecule cro.pdb
[2024-12-11 22:37:53,971 init INFO] [topoaa] Topology CNS input created
[2024-12-11 22:37:53,971 init INFO] [topoaa] Molecule 2: dna.pdb
[2024-12-11 22:37:53,971 init INFO] [topoaa] Sanitizing molecule dna.pdb
[2024-12-11 22:37:53,973 init INFO] [topoaa] Topology CNS input created
[2024-12-11 22:37:53,973 init INFO] [topoaa] Running CNS Jobs n=2
[2024-12-11 22:37:53,973 libutil INFO] Selected 2 cores to process 2 jobs, with 16 maximum available cores.
[2024-12-11 22:37:53,978 libparallel INFO] Using 2 cores
[2024-12-11 22:37:54,365 libparallel INFO] 2 tasks finished
[2024-12-11 22:37:54,365 init INFO] [topoaa] CNS jobs have finished
[2024-12-11 22:37:54,366 base_cns_module INFO] Module [topoaa] finished.
[2024-12-11 22:37:54,366 init INFO] [topoaa] took 0 seconds
[2024-12-11 22:37:54,705 base_cns_module INFO] Running [rigidbody] module
[2024-12-11 22:37:54,706 init INFO] [rigidbody] crossdock=true
[2024-12-11 22:37:54,706 init INFO] [rigidbody] Preparing jobs...
[2024-12-11 22:37:54,706 libutil INFO] Selected 8 cores to process 10 jobs, with 16 maximum available cores.
[2024-12-11 22:37:54,706 libparallel INFO] Using 8 cores
[2024-12-11 22:37:54,719 libparallel INFO] 10 tasks finished
[2024-12-11 22:37:54,720 init INFO] [rigidbody] Preparation took 0.013562 seconds
[2024-12-11 22:37:54,720 init INFO] [rigidbody] Running CNS Jobs n=10
[2024-12-11 22:37:54,720 libutil INFO] Selected 8 cores to process 10 jobs, with 16 maximum available cores.
[2024-12-11 22:37:54,720 libparallel INFO] Using 8 cores
[2024-12-11 22:37:58,938 libparallel INFO] 10 tasks finished
[2024-12-11 22:37:58,938 init INFO] [rigidbody] CNS jobs have finished
[2024-12-11 22:37:58,941 base_cns_module INFO] Module [rigidbody] finished.
[2024-12-11 22:37:58,942 init INFO] [rigidbody] took 4 seconds
[2024-12-11 22:37:58,956 init INFO] Running [caprieval] module
[2024-12-11 22:37:58,956 capri INFO] Found previous CNS step: 01_rigidbody
[2024-12-11 22:37:59,108 capri INFO] Saved scoring weights to: weights_params.json
[2024-12-11 22:37:59,117 libutil INFO] Selected 8 cores to process 10 jobs, with 16 maximum available cores.
[2024-12-11 22:37:59,117 libparallel INFO] Using 8 cores
[2024-12-11 22:37:59,142 libparallel WARNING] Exception in task execution: maximum recursion depth exceeded
[2024-12-11 22:37:59,142 libparallel WARNING] Exception in task execution: maximum recursion depth exceeded
[2024-12-11 22:37:59,142 libparallel WARNING] Exception in task execution: maximum recursion depth exceeded
[2024-12-11 22:37:59,142 libparallel WARNING] Exception in task execution: maximum recursion depth exceeded
[2024-12-11 22:37:59,142 libparallel WARNING] Exception in task execution: maximum recursion depth exceeded
[2024-12-11 22:37:59,148 libparallel WARNING] Exception in task execution: maximum recursion depth exceeded
[2024-12-11 22:37:59,148 libparallel WARNING] Exception in task execution: maximum recursion depth exceeded
[2024-12-11 22:37:59,150 libparallel WARNING] Exception in task execution: maximum recursion depth exceeded
[2024-12-11 22:37:59,150 libparallel WARNING] Exception in task execution: maximum recursion depth exceeded
[2024-12-11 22:37:59,151 libparallel WARNING] Exception in task execution: maximum recursion depth exceeded
[2024-12-11 22:37:59,153 libparallel INFO] 10 tasks finished
[2024-12-11 22:37:59,154 libutil ERROR] 'NoneType' object has no attribute 'identificator'
Traceback (most recent call last):
File "/home/root777/anaconda3/envs/haddock/lib/python3.12/site-packages/haddock/libs/libutil.py", line 335, in log_error_and_exit
yield
File "/home/root777/anaconda3/envs/haddock/lib/python3.12/site-packages/haddock/clis/cli.py", line 195, in main
workflow.run()
File "/home/root777/anaconda3/envs/haddock/lib/python3.12/site-packages/haddock/libs/libworkflow.py", line 43, in run
step.execute()
File "/home/root777/anaconda3/envs/haddock/lib/python3.12/site-packages/haddock/libs/libworkflow.py", line 162, in execute
self.module.run() # type: ignore
^^^^^^^^^^^^^^^^^
File "/home/root777/anaconda3/envs/haddock/lib/python3.12/site-packages/haddock/modules/init.py", line 245, in run
self._run()
File "/home/root777/anaconda3/envs/haddock/lib/python3.12/site-packages/haddock/modules/analysis/caprieval/init.py", line 131, in _run
jobs = sorted(jobs, key=lambda capri: capri.identificator)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/root777/anaconda3/envs/haddock/lib/python3.12/site-packages/haddock/modules/analysis/caprieval/init.py", line 131, in
jobs = sorted(jobs, key=lambda capri: capri.identificator)
^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'identificator'
[2024-12-11 22:37:59,157 libutil ERROR] 'NoneType' object has no attribute 'identificator'
[2024-12-11 22:37:59,157 libutil ERROR] An error has occurred, see log file. And contact the developers if needed.
[2024-12-11 22:37:59,157 libutil INFO] Finished at 11/12/2024 22:37:59. For any help contact us at https://github.com/haddocking/haddock3/issues. Tchau! Do pobachennya! Até logo!.
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