[2025-10-01T01:59:57.938140] [QUERYOME] Starting research for query 1034: 'Instructions: 
 Answer the question below. First, respond with the single best option letter (A, B, C, or D). Then provide a concise reasoning (1–3 sentences). Use both the retrieved evidence and your own medical knowledge to choose the most accurate answer. 

Question:
What is the codon for selenocysteine? 

Options:
{'A': 'UAG', 'B': 'UGA', 'C': 'UAA', 'D': 'GUA'}'
[2025-10-01T01:59:57.989036] [PI] Starting research for query: 'Instructions: 
 Answer the question below. First, respond with the single best option letter (A, B, C, or D). Then provide a concise reasoning (1–3 sentences). Use both the retrieved evidence and your own medical knowledge to choose the most accurate answer. 

Question:
What is the codon for selenocysteine? 

Options:
{'A': 'UAG', 'B': 'UGA', 'C': 'UAA', 'D': 'GUA'}'
[2025-10-01T01:59:57.990604] Saving text to bench_final/run1/medmcqa/medmcqa_1033/pi_initial_prompt.txt
[2025-10-01T01:59:57.999151] [PI] Calling o3 for initial analysis...
[2025-10-01T02:00:02.822859] [PI] Reasoning iteration 1
[2025-10-01T02:00:02.824193] [PI reasoning] **Determining selenocysteine codon**

I need to identify the codon for selenocysteine. It’s actually encoded by the UGA stop codon, but only when a SECIS element is present. So, the answer is B: UGA. I'll need to gather some citations, even for such straightforward information, to back this up. Therefore, I’ll look for an article or source that proves this to provide solid evidence.
[2025-10-01T02:00:02.825661] [PI] Executing function call 1: hybrid_search
[2025-10-01T02:00:02.827858] [PI] Function arguments: {'query': 'selenocysteine codon UGA stop codon', 'k': 5, 'faiss_weight': 0.7, 'bm25_weight': 0.3, 'use_rrf': True}
[2025-10-01T02:00:02.829251] Saving JSON to bench_final/run1/medmcqa/medmcqa_1033/pi_iteration_1_tool_call_2_hybrid_search.json
[2025-10-01T02:00:37.320431] [PI] Function hybrid_search executed successfully
[2025-10-01T02:00:37.322853] Saving JSON to bench_final/run1/medmcqa/medmcqa_1033/pi_iteration_1_tool_result_2_hybrid_search.json
[2025-10-01T02:00:37.350915] [PI] Continuing reasoning with 1 function responses...
[2025-10-01T02:00:41.325646] [PI] Reasoning iteration 2
[2025-10-01T02:00:41.331890] [PI] No function calls found in response
[2025-10-01T02:00:41.336959] [PI] No more function calls - research complete
[2025-10-01T02:00:41.338601] Saving text to bench_final/run1/medmcqa/medmcqa_1033/pi_final_answer.txt
[2025-10-01T02:00:41.343998] [QUERYOME] Query completed successfully
