8000 KrakenUniq: task.cpus not properly inherited? · Issue #613 · nf-core/taxprofiler · GitHub
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KrakenUniq: task.cpus not properly inherited? #613

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AnotherSimon opened this issue May 15, 2025 · 2 comments
Open

KrakenUniq: task.cpus not properly inherited? #613

AnotherSimon opened this issue May 15, 2025 · 2 comments
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@AnotherSimon
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Description of the bug

While trying to run KrakenUniq, I noticed the job was taking forever. Turns out it was using 4 CPU by default.

Tried to overwrite this in a config file as follows:

process {
    withName: 'KRAKENUNIQ.*'  {
        cpus = 32
        memory = 64.GB
    }
}

At run time, it turned out that only the memory requested was correctly updated, not the cpu (from .command.sh):

# Preload the KrakenUniq database into memory.
krakenuniq \
     \
    --db KrakenUniq_MicrobialDB_2023-08-08 \
    --preload \
    --preload-size 64G \
    --threads 4

# Run the KrakenUniq classification on each sample in the batch.
while IFS='     ' read -r SEQ PREFIX; do
    krakenuniq \
        --db KrakenUniq_MicrobialDB_2023-08-08 \
        --threads 4 \
        --report-file "${PREFIX}.krakenuniq.report.txt" \
         \
         \
         \
         \
        "${SEQ}"
done < .inputs.txt

Possibly related to issue #611 ?

Command used and terminal output



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          @AnotherSimon
AnotherSimon




          added
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  bug

  Something isn't working
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      May 15, 2025

    

  








      

  
      



  

  @jfy133





  


    

      

  

    

        
    
    

  


      
          
  
      
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            jfy133
  

      

      

      commented


        May 15, 2025


      
    


  




      


        


  
    

      
          
Hi @AnotherSimon could you provide the command used, and any configs you were using?

      		
    

  





        


            

            
            

              
            

        

      


      

            
  
  

    
  
    
    

  

  

  


    












      

  
      



  

  @jfy133





  


    

      

  

    

        
    
    

  


      
          
  
      
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            jfy133
  

      

      

      commented


        May 22, 2025


      
    


  




      


        


  
    

      
          
I ask as the only time that cpus=4 is set for KrakenUniq is for the -profile test, (by default it runs with 12 CPUS, and is confirmed by the release tests results here: https://nf-co.re/taxprofiler/1.2.2/results/taxprofiler/results-80d2fcce1daeb95c69f16832ca253dbaeac8a11e/pipeline_info/?file=execution_report_2025-03-11_08-35-46.html)


So it makes me wonder if the test command was accidently left in your command somewhere?

      		
    

  





        


            

            
            

              
            

        

      


      

            
  
  

    
  
    
    

  

  

  


    
















  
  

    

      

  





  




  
  

              

  
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