[2025-10-01T22:38:22.018760] [QUERYOME] Starting research for query 1061: '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:
Following are the essential amino acids:

Options:
A. Phenylalanine, Tryptophan, Lysine
B. Phenylalanine, Asparagine, Methionine
C. Phenylalanine, Valine, Glycine
D. Histidine, Glutamine, Valine'
[2025-10-01T22:38:22.058617] [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:
Following are the essential amino acids:

Options:
A. Phenylalanine, Tryptophan, Lysine
B. Phenylalanine, Asparagine, Methionine
C. Phenylalanine, Valine, Glycine
D. Histidine, Glutamine, Valine'
[2025-10-01T22:38:22.060727] Saving text to bench_final/run1/medmcqa/medmcqa_2621/pi_initial_prompt.txt
[2025-10-01T22:38:22.064418] [PI] Calling o3 for initial analysis...
[2025-10-01T22:38:32.596982] [PI] Reasoning iteration 1
[2025-10-01T22:38:32.598623] [PI reasoning] **Identifying essential amino acids**

I’m looking to list essential amino acids for adults, which include Phenylalanine, Valine, Threonine, Tryptophan, Isoleucine, Methionine, Histidine (sometimes viewed as semi-essential), Leucine, and Lysine. For the options presented, I find that option A is entirely correct since it includes only essential amino acids: Phenylalanine, Tryptophan, and Lysine. The other options all contain at least one non-essential amino acid, making them incorrect. I might also find some citations to support this.
[2025-10-01T22:38:32.604792] [PI] Executing function call 1: hybrid_search
[2025-10-01T22:38:32.606633] [PI] Function arguments: {'query': 'essential amino acids phenylalanine tryptophan lysine essential amino acids list', 'k': 10, 'faiss_weight': 0.6, 'bm25_weight': 0.4, 'use_rrf': True}
[2025-10-01T22:38:32.608200] Saving JSON to bench_final/run1/medmcqa/medmcqa_2621/pi_iteration_1_tool_call_2_hybrid_search.json
[2025-10-01T22:38:34.306463] [PI] Function hybrid_search executed successfully
[2025-10-01T22:38:34.308775] Saving JSON to bench_final/run1/medmcqa/medmcqa_2621/pi_iteration_1_tool_result_2_hybrid_search.json
[2025-10-01T22:38:34.314972] [PI] Continuing reasoning with 1 function responses...
[2025-10-01T22:38:43.993176] [PI] Reasoning iteration 2
[2025-10-01T22:38:43.994600] [PI] No function calls found in response
[2025-10-01T22:38:43.996391] [PI] No more function calls - research complete
[2025-10-01T22:38:43.998021] Saving text to bench_final/run1/medmcqa/medmcqa_2621/pi_final_answer.txt
[2025-10-01T22:38:44.022086] [QUERYOME] Query completed successfully
