Return code: 0
Duration: 372.3s

=== STDOUT ===
🚀 Running coder
📦 Dynamic packages: clingo
🤖 Creating agent with model: anthropic/claude-sonnet-4.5
🤖 Using model: anthropic/claude-sonnet-4.5
  python_exec: defining function reverse_complement()
  python_exec: defining function generate_asp_facts()
  python_exec: defining function reverse_complement()
  python_exec: asp_program = """
  python_exec: defining function compute_valid_adjacencies()
  python_exec: print("Fragments that can start contigs (begin wit...
  python_exec: defining function generate_complete_asp_facts()
  python_exec: asp_rules = """
  python_exec: defining function on_model()
  python_exec: print("Valid starting fragments:")
  python_exec: print("Path 1: F0(forward) -> F1(forward) -> F2(fo...
  python_exec: defining function on_model2()
  python_exec: defining function on_model3()
  python_exec: print("Fragments that start with ATG AND end with ...
  python_exec: defining function on_model4()
  python_exec: defining function on_model5()
  python_exec: print("Contig 3: F4(forward) -> F5(reverse) -> F7(...
  python_exec: defining function on_model6()
  python_exec: defining function on_model7()
  python_exec: if len(solutions7) > 1:
  python_exec: defining function reconstruct_sequence()
  python_exec: print("Verification:")
  save_code: {'code': 'import clingo\nimpor...
  python_exec: executing file 047_dna_sequence_assembly_hard_task_code.py
  report_issue: {'text': 'All is fine - no iss...

Perfect! I have successfully completed the DNA fragment assembly task using     
Answer Set Programming. The solution:                                           


                                    Summary                                     

✅ Task Completed Successfully                                                  

The ASP-based solution correctly:                                               

 1 Assembled 8 fragments into 2 contigs (matching the expected minimum)         
 2 Identified F8 as chimeric (cannot form valid contigs with start/stop codon   
   requirements)                                                                
 3 Satisfied all constraints:                                                   
    • Both contigs start with ATG (start codon)                                 
    • Both contigs end with stop codons (TAA and TGA)                           
    • All overlaps meet the minimum requirements (4 bases for high GC pairs, 3  
      bases otherwise)                                                          
    • Fragments can be used in forward or reverse-complement orientation        

Final Output:                                                                   

 • Contig 1: F4(forward) → F5(reverse) → F6(forward) → F7(forward) =            
   ATGCCTCGAGCTGA                                                               
 • Contig 2: F0(forward) → F1(forward) → F2(forward) → F3(forward) =            
   ATGGGCGCCATTTAA                                                              
 • Chimeric: F8                                                                 

The solution uses a two-level optimization strategy: first maximize fragments   
used (minimize chimeric), then minimize the number of contigs.                  

==================================================
📊 Execution Statistics
==================================================

🔧 Tool Usage:
  python_exec           23 calls
  report_issue           1 calls
  save_code              1 calls

💬 Token Consumption:
  Input tokens:        708,490
  Output tokens:       20,909
  Total tokens:        729,399

⏱️  Execution time: 6m 11.2s
==================================================


=== STDERR ===
2025-10-11 19:22:04,824 - coder.kernel - WARNING - Existing kernel is dead, will restart
