mLLM Annotatin of all clusters
Nasir Mahmood Abbasi
2025-06-26
1. load libraries
2. Load Seurat Object
All_samples_Merged <- readRDS("../0-Seurat_RDS_OBJECT_FINAL/All_samples_Merged_Harmony_integrated_HVG_Updated-17-6-2025-final.rds")
3. Annotate with mLLM
# Set up cache directory to speed up processing
cache_dir <- "./mllmcelltype_cache"
dir.create(cache_dir, showWarnings = FALSE, recursive = TRUE)
# Run LLMCelltype annotation with multiple LLM models
api_keys <- list(
openai = Sys.getenv("OPENAI_API_KEY"),
gemini = Sys.getenv("GEMINI_API_KEY"),
grok = Sys.getenv("GROK_API_KEY"),
anthropic = Sys.getenv("ANTHROPIC_API_KEY"),
deepseek = Sys.getenv("DEEPSEEK_API_KEY")
)
# Run consensus annotation with paid models
consensus_results <- interactive_consensus_annotation(
input = pbmc_markers,
tissue_name = "human blood CD4 T cells",
models = c(
"gemini-2.0-flash",
"gemini-1.5-pro",
"qwen-max-2025-01-25",
"grok-3-latest",
"claude-3-7-sonnet-20250219",
"gpt-4o"
),
api_keys = api_keys,
controversy_threshold = 0.6,
entropy_threshold = 1.0,
max_discussion_rounds = 3,
cache_dir = cache_dir
)
{"timestamp":"2025-06-25 17:54:15","session_id":"20250625_173119","level":"INFO","message":"Cache enabled. Using cache directory: ./mllmcelltype_cache","context":{"cache_dir":"./mllmcelltype_cache"},"pid":110158} Cache enabled. Using cache directory: ./mllmcelltype_cache{"timestamp":"2025-06-25 17:54:15","session_id":"20250625_173119","level":"INFO","message":"Phase 1: Getting initial predictions from all models...","context":{"models_count":6,"models":["gemini-2.0-flash","gemini-1.5-pro","qwen-max-2025-01-25","grok-3-latest","claude-3-7-sonnet-20250219","gpt-4o"]},"pid":110158}
Phase 1: Getting initial predictions from all models...{"timestamp":"2025-06-25 17:54:15","session_id":"20250625_173119","level":"INFO","message":"Processing input with model and provider","context":{"model":"gemini-2.0-flash","provider":"gemini"},"pid":110158}
DEBUG: Formatted lines for prompt:
0: CTAG2,MACROD2,WWTR1,IMPG1,CNTLN,BLK,LINC00616,TUBA3C,AGMO,CDH10
1: XCL1,KLRC1,XCL2,KIR2DL4,MT1G,KRT86,KRT81,KLRF2,ITGAD,IGFBP2
2: SYT4,CA2,CCL17,CFI,CA10,IL13,HS3ST1,AC100801.1,C9orf135,AFP
3: RPS4Y1,TCF7,LINC00861,PIK3IP1,LINC01550,TMIGD2,BEX4,ARMH1,EIF1AY,UTY
4: DNAJC12,CSMD1,ENPP2,AC022613.1,AC096577.1,AC004160.1,PTPRD,FOXA2,MGST1,CLIC2
5: TTC29,LINC02752,AC069410.1,SP5,VIPR2,HMGA2,AMPH,ZNF521,DSC1,ARHGEF28
6: THY1,CFI,CA10,HS3ST1,AFP,RANBP17,AC100801.1,C9orf135,AL023574.1,ALKAL2
7: TRAV17,TRAV9-2,MXD3,PLD1,S1PR4,KLHL4,FUT7,SLC2A2,GPR35,RHOBTB3
8: HOXC9,GPAT2,PTCHD1-AS,IRX3,CTDSPL,GPR27,MIR205HG,LHX9,LRP2,PRSS57
9: TBX4,FAM9C,IL4,AC069410.1,CEBPD,PODXL2,SEMA4A,NPTX1,LINC00469,GZMK
10: RPS4Y1,IL7R,SESN3,UTY,PRKY,AC006369.1,USP9Y,IL6R,DDX3Y,EIF1AY
11: S100A4,S100A6,FUCA1,CDKN1A,TRAV17,PTGDR2,TRAV9-2,SAT1,TNFRSF18,S100P
12: AC114977.1,CD40,CCL3,SERPINE1,CSF2,CCL1,GZMB,VCAM1,HSPA1B,DNAJB1
13: OASL,HERC5,IFIT3,IFIT2,NCF2,IFIT1,CSAG3,CXCL10,CFAP54,IFI44
{"timestamp":"2025-06-25 17:54:15","session_id":"20250625_173119","level":"INFO","message":"Initialized gemini processor","context":{"provider":"gemini"},"pid":110158}
{"timestamp":"2025-06-25 17:54:15","session_id":"20250625_173119","level":"INFO","message":"Starting gemini API request","context":{"model":"gemini-2.0-flash","provider":"gemini"},"pid":110158}
{"timestamp":"2025-06-25 17:54:16","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"gemini","chunks_processed":1},"pid":110158}
{"timestamp":"2025-06-25 17:54:16","session_id":"20250625_173119","level":"INFO","message":"Results consolidated successfully","context":{"provider":"gemini","valid_chunks":1,"total_lines":14},"pid":110158}
{"timestamp":"2025-06-25 17:54:16","session_id":"20250625_173119","level":"INFO","message":"API call completed: gemini/gemini-2.0-flash (1.053s)","context":{"provider":"gemini","model":"gemini-2.0-flash","duration_seconds":1.053,"success":true,"tokens":{},"call_count":7},"pid":110158}
{"timestamp":"2025-06-25 17:54:16","session_id":"20250625_173119","level":"INFO","message":"Model response received","context":{"response":["0: Proliferating T cells","1: NK-like T cells","2: Th2 cells","3: Naive T cells (Male)","4: Unknown","5: Unknown","6: Th2 cells","7: T cells","8: Unknown","9: Cytotoxic T cells","10: Naive T cells (Male)","11: Activated T cells","12: Activated T cells","13: Interferon-stimulated T cells"]},"pid":110158}
{"timestamp":"2025-06-25 17:54:16","session_id":"20250625_173119","level":"INFO","message":"Processing input with model and provider","context":{"model":"gemini-1.5-pro","provider":"gemini"},"pid":110158}
DEBUG: Formatted lines for prompt:
0: CTAG2,MACROD2,WWTR1,IMPG1,CNTLN,BLK,LINC00616,TUBA3C,AGMO,CDH10
1: XCL1,KLRC1,XCL2,KIR2DL4,MT1G,KRT86,KRT81,KLRF2,ITGAD,IGFBP2
2: SYT4,CA2,CCL17,CFI,CA10,IL13,HS3ST1,AC100801.1,C9orf135,AFP
3: RPS4Y1,TCF7,LINC00861,PIK3IP1,LINC01550,TMIGD2,BEX4,ARMH1,EIF1AY,UTY
4: DNAJC12,CSMD1,ENPP2,AC022613.1,AC096577.1,AC004160.1,PTPRD,FOXA2,MGST1,CLIC2
5: TTC29,LINC02752,AC069410.1,SP5,VIPR2,HMGA2,AMPH,ZNF521,DSC1,ARHGEF28
6: THY1,CFI,CA10,HS3ST1,AFP,RANBP17,AC100801.1,C9orf135,AL023574.1,ALKAL2
7: TRAV17,TRAV9-2,MXD3,PLD1,S1PR4,KLHL4,FUT7,SLC2A2,GPR35,RHOBTB3
8: HOXC9,GPAT2,PTCHD1-AS,IRX3,CTDSPL,GPR27,MIR205HG,LHX9,LRP2,PRSS57
9: TBX4,FAM9C,IL4,AC069410.1,CEBPD,PODXL2,SEMA4A,NPTX1,LINC00469,GZMK
10: RPS4Y1,IL7R,SESN3,UTY,PRKY,AC006369.1,USP9Y,IL6R,DDX3Y,EIF1AY
11: S100A4,S100A6,FUCA1,CDKN1A,TRAV17,PTGDR2,TRAV9-2,SAT1,TNFRSF18,S100P
12: AC114977.1,CD40,CCL3,SERPINE1,CSF2,CCL1,GZMB,VCAM1,HSPA1B,DNAJB1
13: OASL,HERC5,IFIT3,IFIT2,NCF2,IFIT1,CSAG3,CXCL10,CFAP54,IFI44
{"timestamp":"2025-06-25 17:54:16","session_id":"20250625_173119","level":"INFO","message":"Initialized gemini processor","context":{"provider":"gemini"},"pid":110158}
{"timestamp":"2025-06-25 17:54:16","session_id":"20250625_173119","level":"INFO","message":"Starting gemini API request","context":{"model":"gemini-1.5-pro","provider":"gemini"},"pid":110158} {"timestamp":"2025-06-25 17:54:16","session_id":"20250625_173119","level":"ERROR","message":"Gemini API request failed","context":{"error":"You exceeded your current quota, please check your plan and billing details. For more information on this error, head to: https://ai.google.dev/gemini-api/docs/rate-limits.","provider":"gemini","model":"gemini-1.5-pro","status_code":429},"pid":110158}
{"timestamp":"2025-06-25 17:54:16","session_id":"20250625_173119","level":"ERROR","message":"Failed to process chunk 1: Gemini API request failed: You exceeded your current quota, please check your plan and billing details. For more information on this error, head to: https://ai.google.dev/gemini-api/docs/rate-limits.","context":{"provider":"gemini","model":"gemini-1.5-pro","chunk":1,"error":"Gemini API request failed: You exceeded your current quota, please check your plan and billing details. For more information on this error, head to: https://ai.google.dev/gemini-api/docs/rate-limits."},"pid":110158} {"timestamp":"2025-06-25 17:54:16","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"gemini","chunks_processed":1},"pid":110158} {"timestamp":"2025-06-25 17:54:16","session_id":"20250625_173119","level":"ERROR","message":"No valid responses received","context":{"provider":"gemini","chunks_attempted":1},"pid":110158} {"timestamp":"2025-06-25 17:54:16","session_id":"20250625_173119","level":"INFO","message":"API call completed: gemini/gemini-1.5-pro (0.094s)","context":{"provider":"gemini","model":"gemini-1.5-pro","duration_seconds":0.094,"success":true,"tokens":{},"call_count":8},"pid":110158}
{"timestamp":"2025-06-25 17:54:16","session_id":"20250625_173119","level":"INFO","message":"Model response received","context":{"response":"Error: No valid responses"},"pid":110158} Warning: No API key found for model 'qwen-max-2025-01-25' (provider: qwen). This model will be skipped.{"timestamp":"2025-06-25 17:54:16","session_id":"20250625_173119","level":"WARN","message":"No API key found for model 'qwen-max-2025-01-25' (provider: qwen). This model will be skipped.","context":{"model":"qwen-max-2025-01-25","provider":"qwen"},"pid":110158}
{"timestamp":"2025-06-25 17:54:16","session_id":"20250625_173119","level":"INFO","message":"Processing input with model and provider","context":{"model":"grok-3-latest","provider":"grok"},"pid":110158}
DEBUG: Formatted lines for prompt:
0: CTAG2,MACROD2,WWTR1,IMPG1,CNTLN,BLK,LINC00616,TUBA3C,AGMO,CDH10
1: XCL1,KLRC1,XCL2,KIR2DL4,MT1G,KRT86,KRT81,KLRF2,ITGAD,IGFBP2
2: SYT4,CA2,CCL17,CFI,CA10,IL13,HS3ST1,AC100801.1,C9orf135,AFP
3: RPS4Y1,TCF7,LINC00861,PIK3IP1,LINC01550,TMIGD2,BEX4,ARMH1,EIF1AY,UTY
4: DNAJC12,CSMD1,ENPP2,AC022613.1,AC096577.1,AC004160.1,PTPRD,FOXA2,MGST1,CLIC2
5: TTC29,LINC02752,AC069410.1,SP5,VIPR2,HMGA2,AMPH,ZNF521,DSC1,ARHGEF28
6: THY1,CFI,CA10,HS3ST1,AFP,RANBP17,AC100801.1,C9orf135,AL023574.1,ALKAL2
7: TRAV17,TRAV9-2,MXD3,PLD1,S1PR4,KLHL4,FUT7,SLC2A2,GPR35,RHOBTB3
8: HOXC9,GPAT2,PTCHD1-AS,IRX3,CTDSPL,GPR27,MIR205HG,LHX9,LRP2,PRSS57
9: TBX4,FAM9C,IL4,AC069410.1,CEBPD,PODXL2,SEMA4A,NPTX1,LINC00469,GZMK
10: RPS4Y1,IL7R,SESN3,UTY,PRKY,AC006369.1,USP9Y,IL6R,DDX3Y,EIF1AY
11: S100A4,S100A6,FUCA1,CDKN1A,TRAV17,PTGDR2,TRAV9-2,SAT1,TNFRSF18,S100P
12: AC114977.1,CD40,CCL3,SERPINE1,CSF2,CCL1,GZMB,VCAM1,HSPA1B,DNAJB1
13: OASL,HERC5,IFIT3,IFIT2,NCF2,IFIT1,CSAG3,CXCL10,CFAP54,IFI44
{"timestamp":"2025-06-25 17:54:16","session_id":"20250625_173119","level":"INFO","message":"Initialized grok processor","context":{"provider":"grok"},"pid":110158}
{"timestamp":"2025-06-25 17:54:16","session_id":"20250625_173119","level":"INFO","message":"Starting grok API request","context":{"model":"grok-3-latest","provider":"grok"},"pid":110158} {"timestamp":"2025-06-25 17:54:17","session_id":"20250625_173119","level":"ERROR","message":"Failed to process chunk 1: $ operator is invalid for atomic vectors","context":{"provider":"grok","model":"grok-3-latest","chunk":1,"error":"$ operator is invalid for atomic vectors"},"pid":110158} {"timestamp":"2025-06-25 17:54:17","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"grok","chunks_processed":1},"pid":110158} {"timestamp":"2025-06-25 17:54:17","session_id":"20250625_173119","level":"ERROR","message":"No valid responses received","context":{"provider":"grok","chunks_attempted":1},"pid":110158} {"timestamp":"2025-06-25 17:54:17","session_id":"20250625_173119","level":"INFO","message":"API call completed: grok/grok-3-latest (0.198s)","context":{"provider":"grok","model":"grok-3-latest","duration_seconds":0.198,"success":true,"tokens":{},"call_count":9},"pid":110158}
{"timestamp":"2025-06-25 17:54:17","session_id":"20250625_173119","level":"INFO","message":"Model response received","context":{"response":"Error: No valid responses"},"pid":110158}
{"timestamp":"2025-06-25 17:54:17","session_id":"20250625_173119","level":"INFO","message":"Processing input with model and provider","context":{"model":"claude-3-7-sonnet-20250219","provider":"anthropic"},"pid":110158}
DEBUG: Formatted lines for prompt:
0: CTAG2,MACROD2,WWTR1,IMPG1,CNTLN,BLK,LINC00616,TUBA3C,AGMO,CDH10
1: XCL1,KLRC1,XCL2,KIR2DL4,MT1G,KRT86,KRT81,KLRF2,ITGAD,IGFBP2
2: SYT4,CA2,CCL17,CFI,CA10,IL13,HS3ST1,AC100801.1,C9orf135,AFP
3: RPS4Y1,TCF7,LINC00861,PIK3IP1,LINC01550,TMIGD2,BEX4,ARMH1,EIF1AY,UTY
4: DNAJC12,CSMD1,ENPP2,AC022613.1,AC096577.1,AC004160.1,PTPRD,FOXA2,MGST1,CLIC2
5: TTC29,LINC02752,AC069410.1,SP5,VIPR2,HMGA2,AMPH,ZNF521,DSC1,ARHGEF28
6: THY1,CFI,CA10,HS3ST1,AFP,RANBP17,AC100801.1,C9orf135,AL023574.1,ALKAL2
7: TRAV17,TRAV9-2,MXD3,PLD1,S1PR4,KLHL4,FUT7,SLC2A2,GPR35,RHOBTB3
8: HOXC9,GPAT2,PTCHD1-AS,IRX3,CTDSPL,GPR27,MIR205HG,LHX9,LRP2,PRSS57
9: TBX4,FAM9C,IL4,AC069410.1,CEBPD,PODXL2,SEMA4A,NPTX1,LINC00469,GZMK
10: RPS4Y1,IL7R,SESN3,UTY,PRKY,AC006369.1,USP9Y,IL6R,DDX3Y,EIF1AY
11: S100A4,S100A6,FUCA1,CDKN1A,TRAV17,PTGDR2,TRAV9-2,SAT1,TNFRSF18,S100P
12: AC114977.1,CD40,CCL3,SERPINE1,CSF2,CCL1,GZMB,VCAM1,HSPA1B,DNAJB1
13: OASL,HERC5,IFIT3,IFIT2,NCF2,IFIT1,CSAG3,CXCL10,CFAP54,IFI44
{"timestamp":"2025-06-25 17:54:17","session_id":"20250625_173119","level":"INFO","message":"Initialized anthropic processor","context":{"provider":"anthropic"},"pid":110158}
{"timestamp":"2025-06-25 17:54:17","session_id":"20250625_173119","level":"INFO","message":"Starting anthropic API request","context":{"model":"claude-3-7-sonnet-20250219","provider":"anthropic"},"pid":110158} {"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"ERROR","message":"Anthropic API request failed","context":{"provider":"anthropic","model":"claude-3-7-sonnet-20250219","status_code":400,"error":"Your credit balance is too low to access the Anthropic API. Please go to Plans & Billing to upgrade or purchase credits."},"pid":110158}
{"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"ERROR","message":"Failed to process chunk 1: Anthropic API request failed: Your credit balance is too low to access the Anthropic API. Please go to Plans & Billing to upgrade or purchase credits.","context":{"provider":"anthropic","model":"claude-3-7-sonnet-20250219","chunk":1,"error":"Anthropic API request failed: Your credit balance is too low to access the Anthropic API. Please go to Plans & Billing to upgrade or purchase credits."},"pid":110158} {"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"anthropic","chunks_processed":1},"pid":110158} {"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"ERROR","message":"No valid responses received","context":{"provider":"anthropic","chunks_attempted":1},"pid":110158} {"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"INFO","message":"API call completed: anthropic/claude-3-7-sonnet-20250219 (1.050s)","context":{"provider":"anthropic","model":"claude-3-7-sonnet-20250219","duration_seconds":1.05,"success":true,"tokens":{},"call_count":10},"pid":110158}
{"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"INFO","message":"Model response received","context":{"response":"Error: No valid responses"},"pid":110158}
{"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"INFO","message":"Processing input with model and provider","context":{"model":"gpt-4o","provider":"openai"},"pid":110158}
DEBUG: Formatted lines for prompt:
0: CTAG2,MACROD2,WWTR1,IMPG1,CNTLN,BLK,LINC00616,TUBA3C,AGMO,CDH10
1: XCL1,KLRC1,XCL2,KIR2DL4,MT1G,KRT86,KRT81,KLRF2,ITGAD,IGFBP2
2: SYT4,CA2,CCL17,CFI,CA10,IL13,HS3ST1,AC100801.1,C9orf135,AFP
3: RPS4Y1,TCF7,LINC00861,PIK3IP1,LINC01550,TMIGD2,BEX4,ARMH1,EIF1AY,UTY
4: DNAJC12,CSMD1,ENPP2,AC022613.1,AC096577.1,AC004160.1,PTPRD,FOXA2,MGST1,CLIC2
5: TTC29,LINC02752,AC069410.1,SP5,VIPR2,HMGA2,AMPH,ZNF521,DSC1,ARHGEF28
6: THY1,CFI,CA10,HS3ST1,AFP,RANBP17,AC100801.1,C9orf135,AL023574.1,ALKAL2
7: TRAV17,TRAV9-2,MXD3,PLD1,S1PR4,KLHL4,FUT7,SLC2A2,GPR35,RHOBTB3
8: HOXC9,GPAT2,PTCHD1-AS,IRX3,CTDSPL,GPR27,MIR205HG,LHX9,LRP2,PRSS57
9: TBX4,FAM9C,IL4,AC069410.1,CEBPD,PODXL2,SEMA4A,NPTX1,LINC00469,GZMK
10: RPS4Y1,IL7R,SESN3,UTY,PRKY,AC006369.1,USP9Y,IL6R,DDX3Y,EIF1AY
11: S100A4,S100A6,FUCA1,CDKN1A,TRAV17,PTGDR2,TRAV9-2,SAT1,TNFRSF18,S100P
12: AC114977.1,CD40,CCL3,SERPINE1,CSF2,CCL1,GZMB,VCAM1,HSPA1B,DNAJB1
13: OASL,HERC5,IFIT3,IFIT2,NCF2,IFIT1,CSAG3,CXCL10,CFAP54,IFI44
{"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"INFO","message":"Initialized openai processor","context":{"provider":"openai"},"pid":110158}
{"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"INFO","message":"Starting openai API request","context":{"model":"gpt-4o","provider":"openai"},"pid":110158} {"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"ERROR","message":"OpenAI API request failed","context":{"error":"You exceeded your current quota, please check your plan and billing details. For more information on this error, read the docs: https://platform.openai.com/docs/guides/error-codes/api-errors.","provider":"openai","model":"gpt-4o","status_code":429},"pid":110158}
{"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"ERROR","message":"Failed to process chunk 1: OpenAI API request failed: You exceeded your current quota, please check your plan and billing details. For more information on this error, read the docs: https://platform.openai.com/docs/guides/error-codes/api-errors.","context":{"provider":"openai","model":"gpt-4o","chunk":1,"error":"OpenAI API request failed: You exceeded your current quota, please check your plan and billing details. For more information on this error, read the docs: https://platform.openai.com/docs/guides/error-codes/api-errors."},"pid":110158} {"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"openai","chunks_processed":1},"pid":110158} {"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"ERROR","message":"No valid responses received","context":{"provider":"openai","chunks_attempted":1},"pid":110158} {"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"INFO","message":"API call completed: openai/gpt-4o (0.633s)","context":{"provider":"openai","model":"gpt-4o","duration_seconds":0.633,"success":true,"tokens":{},"call_count":11},"pid":110158}
{"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"INFO","message":"Model response received","context":{"response":"Error: No valid responses"},"pid":110158}
{"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"INFO","message":"No consensus_check_model specified, using gemini-2.0-flash","context":{"consensus_check_model":"gemini-2.0-flash"},"pid":110158}
{"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"INFO","message":"Phase 2: Identifying controversial clusters...","context":{"clusters_count":14,"entropy_threshold":1,"controversy_threshold":0.6},"pid":110158}
Phase 2: Identifying controversial clusters...{"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"INFO","message":"Analyzing cluster 0...","context":{"cluster_id":"0"},"pid":110158}
Analyzing cluster 0...{"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"INFO","message":"Starting check_consensus function","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"INFO","message":"Starting with simple consensus calculation","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"INFO","message":"CONSENSUS ACHIEVED WITH SIMPLE CHECK - NO LLM NEEDED","context":{"proportion":0.8,"entropy":0.7219,"controversy_threshold":0.6,"entropy_threshold":1,"majority":"No valid responses"},"pid":110158} Cluster consensus achieved via SIMPLE CHECK: No valid responses (CP=0.80, H=0.72){"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"INFO","message":"Consensus reached for cluster 0","context":{"cluster_id":"0","consensus_proportion":0.8,"entropy":0.7219,"selected_cell_type":"No valid responses"},"pid":110158} Consensus reached for cluster 0 (consensus proportion: 0.80, entropy: 0.72, selected: No valid responses){"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"INFO","message":"Analyzing cluster 1...","context":{"cluster_id":"1"},"pid":110158}
Analyzing cluster 1...{"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"INFO","message":"Starting check_consensus function","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"WARN","message":"Not enough responses to check consensus","context":{"response_count":1},"pid":110158}
{"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"INFO","message":"Cluster 1 marked as controversial","context":{"cluster_id":"1","reached_consensus":false,"consensus_proportion":0,"entropy":0},"pid":110158} Cluster 1 marked as controversial (reached: FALSE, consensus proportion: 0.00, entropy: 0.00){"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"INFO","message":"Analyzing cluster 2...","context":{"cluster_id":"2"},"pid":110158}
Analyzing cluster 2...{"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"INFO","message":"Starting check_consensus function","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"WARN","message":"Not enough responses to check consensus","context":{"response_count":1},"pid":110158}
{"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"INFO","message":"Cluster 2 marked as controversial","context":{"cluster_id":"2","reached_consensus":false,"consensus_proportion":0,"entropy":0},"pid":110158} Cluster 2 marked as controversial (reached: FALSE, consensus proportion: 0.00, entropy: 0.00){"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"INFO","message":"Analyzing cluster 3...","context":{"cluster_id":"3"},"pid":110158}
Analyzing cluster 3...{"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"INFO","message":"Starting check_consensus function","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"WARN","message":"Not enough responses to check consensus","context":{"response_count":1},"pid":110158}
{"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"INFO","message":"Cluster 3 marked as controversial","context":{"cluster_id":"3","reached_consensus":false,"consensus_proportion":0,"entropy":0},"pid":110158} Cluster 3 marked as controversial (reached: FALSE, consensus proportion: 0.00, entropy: 0.00){"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"INFO","message":"Analyzing cluster 4...","context":{"cluster_id":"4"},"pid":110158}
Analyzing cluster 4...{"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"INFO","message":"Starting check_consensus function","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"WARN","message":"Not enough responses to check consensus","context":{"response_count":1},"pid":110158}
{"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"INFO","message":"Cluster 4 marked as controversial","context":{"cluster_id":"4","reached_consensus":false,"consensus_proportion":0,"entropy":0},"pid":110158} Cluster 4 marked as controversial (reached: FALSE, consensus proportion: 0.00, entropy: 0.00){"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"INFO","message":"Analyzing cluster 5...","context":{"cluster_id":"5"},"pid":110158}
Analyzing cluster 5...{"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"INFO","message":"Starting check_consensus function","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"WARN","message":"Not enough responses to check consensus","context":{"response_count":1},"pid":110158}
{"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"INFO","message":"Cluster 5 marked as controversial","context":{"cluster_id":"5","reached_consensus":false,"consensus_proportion":0,"entropy":0},"pid":110158} Cluster 5 marked as controversial (reached: FALSE, consensus proportion: 0.00, entropy: 0.00){"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"INFO","message":"Analyzing cluster 6...","context":{"cluster_id":"6"},"pid":110158}
Analyzing cluster 6...{"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"INFO","message":"Starting check_consensus function","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"WARN","message":"Not enough responses to check consensus","context":{"response_count":1},"pid":110158}
{"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"INFO","message":"Cluster 6 marked as controversial","context":{"cluster_id":"6","reached_consensus":false,"consensus_proportion":0,"entropy":0},"pid":110158} Cluster 6 marked as controversial (reached: FALSE, consensus proportion: 0.00, entropy: 0.00){"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"INFO","message":"Analyzing cluster 7...","context":{"cluster_id":"7"},"pid":110158}
Analyzing cluster 7...{"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"INFO","message":"Starting check_consensus function","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"WARN","message":"Not enough responses to check consensus","context":{"response_count":1},"pid":110158}
{"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"INFO","message":"Cluster 7 marked as controversial","context":{"cluster_id":"7","reached_consensus":false,"consensus_proportion":0,"entropy":0},"pid":110158} Cluster 7 marked as controversial (reached: FALSE, consensus proportion: 0.00, entropy: 0.00){"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"INFO","message":"Analyzing cluster 8...","context":{"cluster_id":"8"},"pid":110158}
Analyzing cluster 8...{"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"INFO","message":"Starting check_consensus function","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"WARN","message":"Not enough responses to check consensus","context":{"response_count":1},"pid":110158}
{"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"INFO","message":"Cluster 8 marked as controversial","context":{"cluster_id":"8","reached_consensus":false,"consensus_proportion":0,"entropy":0},"pid":110158} Cluster 8 marked as controversial (reached: FALSE, consensus proportion: 0.00, entropy: 0.00){"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"INFO","message":"Analyzing cluster 9...","context":{"cluster_id":"9"},"pid":110158}
Analyzing cluster 9...{"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"INFO","message":"Starting check_consensus function","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"WARN","message":"Not enough responses to check consensus","context":{"response_count":1},"pid":110158}
{"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"INFO","message":"Cluster 9 marked as controversial","context":{"cluster_id":"9","reached_consensus":false,"consensus_proportion":0,"entropy":0},"pid":110158} Cluster 9 marked as controversial (reached: FALSE, consensus proportion: 0.00, entropy: 0.00){"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"INFO","message":"Analyzing cluster 10...","context":{"cluster_id":"10"},"pid":110158}
Analyzing cluster 10...{"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"INFO","message":"Starting check_consensus function","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"WARN","message":"Not enough responses to check consensus","context":{"response_count":1},"pid":110158}
{"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"INFO","message":"Cluster 10 marked as controversial","context":{"cluster_id":"10","reached_consensus":false,"consensus_proportion":0,"entropy":0},"pid":110158} Cluster 10 marked as controversial (reached: FALSE, consensus proportion: 0.00, entropy: 0.00){"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"INFO","message":"Analyzing cluster 11...","context":{"cluster_id":"11"},"pid":110158}
Analyzing cluster 11...{"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"INFO","message":"Starting check_consensus function","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"WARN","message":"Not enough responses to check consensus","context":{"response_count":1},"pid":110158}
{"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"INFO","message":"Cluster 11 marked as controversial","context":{"cluster_id":"11","reached_consensus":false,"consensus_proportion":0,"entropy":0},"pid":110158} Cluster 11 marked as controversial (reached: FALSE, consensus proportion: 0.00, entropy: 0.00){"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"INFO","message":"Analyzing cluster 12...","context":{"cluster_id":"12"},"pid":110158}
Analyzing cluster 12...{"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"INFO","message":"Starting check_consensus function","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"WARN","message":"Not enough responses to check consensus","context":{"response_count":1},"pid":110158}
{"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"INFO","message":"Cluster 12 marked as controversial","context":{"cluster_id":"12","reached_consensus":false,"consensus_proportion":0,"entropy":0},"pid":110158} Cluster 12 marked as controversial (reached: FALSE, consensus proportion: 0.00, entropy: 0.00){"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"INFO","message":"Analyzing cluster 13...","context":{"cluster_id":"13"},"pid":110158}
Analyzing cluster 13...{"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"INFO","message":"Starting check_consensus function","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"WARN","message":"Not enough responses to check consensus","context":{"response_count":1},"pid":110158}
{"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"INFO","message":"Cluster 13 marked as controversial","context":{"cluster_id":"13","reached_consensus":false,"consensus_proportion":0,"entropy":0},"pid":110158} Cluster 13 marked as controversial (reached: FALSE, consensus proportion: 0.00, entropy: 0.00){"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"INFO","message":"Phase 3: Starting discussions for 13 controversial clusters...","context":{"controversial_count":13,"clusters":["1","2","3","4","5","6","7","8","9","10","11","12","13"]},"pid":110158}
Phase 3: Starting discussions for 13 controversial clusters...{"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"INFO","message":"Starting discussion for cluster 1...","context":{"cluster_id":"1"},"pid":110158}
Starting discussion for cluster 1...{"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"INFO","message":"Discussion start for cluster 1","context":{"cluster_id":"1","event_type":"start","data":{"tissue_name":"human blood CD4 T cells","marker_genes":"XCL1,KIR3DL1,KLRC1,EPCAM,MATK,XCL2,MYO1E,KIR2DL4,TRGV2,TRAV38-2DV8"}},"pid":110158}
{"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"INFO","message":"Initialized gemini processor","context":{"provider":"gemini"},"pid":110158}
{"timestamp":"2025-06-25 17:54:18","session_id":"20250625_173119","level":"INFO","message":"Starting gemini API request","context":{"model":"gemini-2.0-flash","provider":"gemini"},"pid":110158}
{"timestamp":"2025-06-25 17:54:28","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"gemini","chunks_processed":1},"pid":110158}
{"timestamp":"2025-06-25 17:54:28","session_id":"20250625_173119","level":"INFO","message":"Results consolidated successfully","context":{"provider":"gemini","valid_chunks":1,"total_lines":30},"pid":110158}
{"timestamp":"2025-06-25 17:54:28","session_id":"20250625_173119","level":"INFO","message":"API call completed: gemini/gemini-2.0-flash (10.001s)","context":{"provider":"gemini","model":"gemini-2.0-flash","duration_seconds":10.001,"success":true,"tokens":{},"call_count":12},"pid":110158}
{"timestamp":"2025-06-25 17:54:28","session_id":"20250625_173119","level":"INFO","message":"API call completed: gemini/gemini-2.0-flash (10.002s)","context":{"provider":"gemini","model":"gemini-2.0-flash","duration_seconds":10.002,"success":true,"tokens":{},"call_count":13},"pid":110158}
{"timestamp":"2025-06-25 17:54:28","session_id":"20250625_173119","level":"INFO","message":"Model response received successfully","context":{"provider":"gemini","model":"gemini-2.0-flash","response_length":[79,0,135,0,1002,0,8,483,219,216,359,219,138,0,574,0,9,450,738,230,0,11,0,170,162,280,90,148,218,149],"duration_seconds":10.002},"pid":110158}
{"timestamp":"2025-06-25 17:54:28","session_id":"20250625_173119","level":"INFO","message":"Discussion prediction for cluster 1","context":{"cluster_id":"1","event_type":"prediction","data":{"model":"gemini-2.0-flash","round":1,"prediction":["CELL TYPE: **NK-like T cells, likely cytotoxic T cells with NK cell receptors**","","GROUNDS: The cluster expresses the following marker genes: XCL1, KIR3DL1, KLRC1, EPCAM, MATK, XCL2, MYO1E, KIR2DL4, TRGV2, TRAV38-2DV8.","","WARRANT: This combination of markers suggests a population of T cells that possess characteristics of both conventional T cells and Natural Killer (NK) cells. The presence of T cell receptor genes (TRGV2, TRAV38-2DV8) definitively identifies the cells as T cells. The presence of KIR (Killer-cell Immunoglobulin-like Receptor) genes (KIR3DL1, KIR2DL4) and KLRC1 (NKG2A) are characteristic of NK cells, but can also be expressed by specialized subsets of T cells, particularly cytotoxic T cells. XCL1 and XCL2 are chemokines involved in attracting other immune cells, consistent with a cytotoxic function. MYO1E is involved in actin dynamics, likely playing a role in cytotoxicity. MATK is a tyrosine kinase involved in T cell signaling. EPCAM, while more commonly associated with epithelial cells, has been shown to be expressed in some hematopoietic cells including activated T cells, especially in tumors but sometimes also in peripheral blood, and can play a role in T cell activation and migration.","","BACKING:","* **KIR genes (KIR3DL1, KIR2DL4):** KIRs are typically associated with NK cells where they regulate cytotoxicity by interacting with MHC class I molecules on target cells (Vivier et al., 2011; Lanier, 2005). However, KIR expression has been observed on subsets of CD8+ T cells, particularly in the context of viral infections and aging (van den Broek et al., 2023; Geginat et al., 2016). These KIR+ T cells often exhibit enhanced cytotoxic potential and altered effector functions.","* **KLRC1 (NKG2A):** NKG2A is another inhibitory receptor expressed by NK cells and some T cells, further suggesting NK-like characteristics. It forms a heterodimer with CD94 and recognizes HLA-E (Braud et al., 1998).","* **XCL1 and XCL2:** These chemokines recruit NK cells and other cytotoxic lymphocytes. Their expression indicates a role in immune surveillance and recruitment of other immune cells to sites of infection or tumor.","* **EPCAM:** While primarily epithelial, EPCAM expression has been reported on activated T cells, contributing to their adhesion and migration capabilities, particularly in the context of inflammation or cancer (Fong et al., 2013; Munz et al., 2009). Though unexpected, its expression here does not negate the T cell identity defined by TCR gene expression.","* **MYO1E:** This gene encodes a myosin involved in actin remodeling, a process vital for T cell migration, synapse formation, and cytotoxic granule release. Its presence supports the likelihood of cytotoxic function.","* **TRGV2 and TRAV38-2DV8:** These are T cell receptor variable region genes, confirming the T cell lineage of the cells in the cluster.","","QUALIFIER: **Probable**. While the presence of TCR genes definitively confirms T cell identity, the co-expression of NK cell receptors (KIRs, NKG2A) makes the \"NK-like T cell\" classification highly probable. The exact functional role and differentiation state of these cells would require further investigation, such as assessing their cytotoxic activity and cytokine production. The expression of EPCAM is less common for circulating T cells, so further investigation might be needed to ensure it is not a result of sample contamination or a very specific activation state.","","REBUTTAL:","* **Alternative interpretations of KIR and NKG2A expression:** While KIRs and NKG2A are primarily associated with NK cells, their expression on T cells is well-documented. It's possible that these cells represent a subset of T cells that have undergone a process of NK-like differentiation or have acquired NK cell-like functions. The lack of additional NK cell-specific markers (e.g., CD56 without CD3) makes a pure NK cell population less likely.","* **Model disagreements:** The lack of prediction from other models highlights the complexity of cell type classification based on gene expression data. It is possible that these models were trained on datasets that did not include or underrepresented this particular T cell subset. However, the consistent co-expression of T cell receptor genes with NK cell receptors provides strong evidence for the NK-like T cell identity. The Gemini-2.0-flash model correctly predicted NK-like T cells, lending credence to the overall assessment. The absence of prediction from other models might be due to their conservative algorithms not labeling a cell type without high confidence, especially when encountering less common marker combinations.","* **EPCAM: an unexpected find**: the presence of EPCAM requires further investigation to ensure its origin and role. But, recent studies have demonstrated its presence on activated T cells, especially in inflammatory conditions.","","REFERENCES:","","* Braud, V. M., Jones, E. Y., & McMichael, A. J. (1998). The human major histocompatibility complex class Ib molecule HLA-E. *Annual Review of Immunology, 16*, 483-516.","* Fong, C. W., Stewart, T. J., & Mercer, A. A. (2013). EpCAM: a review of its expression and roles in normal and malignant tissues. *Pathology, 45*(5), 443-453.","* Geginat, J., Zingoni, A., Palmieri, G., Refolo, G., Kaderi, A., Capone, I., ... & Santoni, A. (2016). Human CD8+ T cells expressing the killer cell lectin-like receptor G1 constitute a distinct subset with markedly reduced proliferative potential. *Blood, 127*(24), 3067-3077.","* Lanier, L. L. (2005). NK cell recognition. *Annual Review of Immunology, 23*, 225-274.","* Munz, M., Baeuerle, P. A., Gires, O. (2009). The emerging role of EpCAM in cancer and stem cell signaling. *Cancer Research, 69*(14), 5627-5629.","* van den Broek, T., Heijhuijs, N. A., van Aalst, C. W., de Boer, R. J., Borghans, J. A. M., & Geginat, J. (2023). The Dynamics of KIR Expression on Human T Cells and NK Cells. *Frontiers in Immunology, 14*, 1145953.","* Vivier, E., Tomasello, E., Baratin, M., Walzer, T., & Ugolini, S. (2011). Functions of natural killer cells. *Nature Immunology, 12*(6), 451-458."]}},"pid":110158}
{"timestamp":"2025-06-25 17:54:28","session_id":"20250625_173119","level":"INFO","message":"Initialized gemini processor","context":{"provider":"gemini"},"pid":110158}
{"timestamp":"2025-06-25 17:54:28","session_id":"20250625_173119","level":"INFO","message":"Starting gemini API request","context":{"model":"gemini-1.5-pro","provider":"gemini"},"pid":110158} {"timestamp":"2025-06-25 17:54:28","session_id":"20250625_173119","level":"ERROR","message":"Gemini API request failed","context":{"error":"You exceeded your current quota, please check your plan and billing details. For more information on this error, head to: https://ai.google.dev/gemini-api/docs/rate-limits.","provider":"gemini","model":"gemini-1.5-pro","status_code":429},"pid":110158}
{"timestamp":"2025-06-25 17:54:28","session_id":"20250625_173119","level":"ERROR","message":"Failed to process chunk 1: Gemini API request failed: You exceeded your current quota, please check your plan and billing details. For more information on this error, head to: https://ai.google.dev/gemini-api/docs/rate-limits.","context":{"provider":"gemini","model":"gemini-1.5-pro","chunk":1,"error":"Gemini API request failed: You exceeded your current quota, please check your plan and billing details. For more information on this error, head to: https://ai.google.dev/gemini-api/docs/rate-limits."},"pid":110158} {"timestamp":"2025-06-25 17:54:29","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"gemini","chunks_processed":1},"pid":110158} {"timestamp":"2025-06-25 17:54:29","session_id":"20250625_173119","level":"ERROR","message":"No valid responses received","context":{"provider":"gemini","chunks_attempted":1},"pid":110158} {"timestamp":"2025-06-25 17:54:29","session_id":"20250625_173119","level":"INFO","message":"API call completed: gemini/gemini-1.5-pro (0.064s)","context":{"provider":"gemini","model":"gemini-1.5-pro","duration_seconds":0.064,"success":true,"tokens":{},"call_count":14},"pid":110158}
{"timestamp":"2025-06-25 17:54:29","session_id":"20250625_173119","level":"INFO","message":"API call completed: gemini/gemini-1.5-pro (0.066s)","context":{"provider":"gemini","model":"gemini-1.5-pro","duration_seconds":0.066,"success":true,"tokens":{},"call_count":15},"pid":110158}
{"timestamp":"2025-06-25 17:54:29","session_id":"20250625_173119","level":"INFO","message":"Model response received successfully","context":{"provider":"gemini","model":"gemini-1.5-pro","response_length":25,"duration_seconds":0.066},"pid":110158}
{"timestamp":"2025-06-25 17:54:29","session_id":"20250625_173119","level":"INFO","message":"Discussion prediction for cluster 1","context":{"cluster_id":"1","event_type":"prediction","data":{"model":"gemini-1.5-pro","round":1,"prediction":"Error: No valid responses"}},"pid":110158}
{"timestamp":"2025-06-25 17:54:29","session_id":"20250625_173119","level":"INFO","message":"Initialized grok processor","context":{"provider":"grok"},"pid":110158}
{"timestamp":"2025-06-25 17:54:29","session_id":"20250625_173119","level":"INFO","message":"Starting grok API request","context":{"model":"grok-3-latest","provider":"grok"},"pid":110158} {"timestamp":"2025-06-25 17:54:29","session_id":"20250625_173119","level":"ERROR","message":"Failed to process chunk 1: $ operator is invalid for atomic vectors","context":{"provider":"grok","model":"grok-3-latest","chunk":1,"error":"$ operator is invalid for atomic vectors"},"pid":110158} {"timestamp":"2025-06-25 17:54:29","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"grok","chunks_processed":1},"pid":110158} {"timestamp":"2025-06-25 17:54:29","session_id":"20250625_173119","level":"ERROR","message":"No valid responses received","context":{"provider":"grok","chunks_attempted":1},"pid":110158} {"timestamp":"2025-06-25 17:54:29","session_id":"20250625_173119","level":"INFO","message":"API call completed: grok/grok-3-latest (0.274s)","context":{"provider":"grok","model":"grok-3-latest","duration_seconds":0.274,"success":true,"tokens":{},"call_count":16},"pid":110158}
{"timestamp":"2025-06-25 17:54:29","session_id":"20250625_173119","level":"INFO","message":"API call completed: grok/grok-3-latest (0.276s)","context":{"provider":"grok","model":"grok-3-latest","duration_seconds":0.276,"success":true,"tokens":{},"call_count":17},"pid":110158}
{"timestamp":"2025-06-25 17:54:29","session_id":"20250625_173119","level":"INFO","message":"Model response received successfully","context":{"provider":"grok","model":"grok-3-latest","response_length":25,"duration_seconds":0.276},"pid":110158}
{"timestamp":"2025-06-25 17:54:29","session_id":"20250625_173119","level":"INFO","message":"Discussion prediction for cluster 1","context":{"cluster_id":"1","event_type":"prediction","data":{"model":"grok-3-latest","round":1,"prediction":"Error: No valid responses"}},"pid":110158}
{"timestamp":"2025-06-25 17:54:29","session_id":"20250625_173119","level":"INFO","message":"Initialized anthropic processor","context":{"provider":"anthropic"},"pid":110158}
{"timestamp":"2025-06-25 17:54:29","session_id":"20250625_173119","level":"INFO","message":"Starting anthropic API request","context":{"model":"claude-3-7-sonnet-20250219","provider":"anthropic"},"pid":110158} {"timestamp":"2025-06-25 17:54:29","session_id":"20250625_173119","level":"ERROR","message":"Anthropic API request failed","context":{"provider":"anthropic","model":"claude-3-7-sonnet-20250219","status_code":400,"error":"Your credit balance is too low to access the Anthropic API. Please go to Plans & Billing to upgrade or purchase credits."},"pid":110158}
{"timestamp":"2025-06-25 17:54:29","session_id":"20250625_173119","level":"ERROR","message":"Failed to process chunk 1: Anthropic API request failed: Your credit balance is too low to access the Anthropic API. Please go to Plans & Billing to upgrade or purchase credits.","context":{"provider":"anthropic","model":"claude-3-7-sonnet-20250219","chunk":1,"error":"Anthropic API request failed: Your credit balance is too low to access the Anthropic API. Please go to Plans & Billing to upgrade or purchase credits."},"pid":110158} {"timestamp":"2025-06-25 17:54:29","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"anthropic","chunks_processed":1},"pid":110158} {"timestamp":"2025-06-25 17:54:29","session_id":"20250625_173119","level":"ERROR","message":"No valid responses received","context":{"provider":"anthropic","chunks_attempted":1},"pid":110158} {"timestamp":"2025-06-25 17:54:29","session_id":"20250625_173119","level":"INFO","message":"API call completed: anthropic/claude-3-7-sonnet-20250219 (0.149s)","context":{"provider":"anthropic","model":"claude-3-7-sonnet-20250219","duration_seconds":0.149,"success":true,"tokens":{},"call_count":18},"pid":110158}
{"timestamp":"2025-06-25 17:54:29","session_id":"20250625_173119","level":"INFO","message":"API call completed: anthropic/claude-3-7-sonnet-20250219 (0.151s)","context":{"provider":"anthropic","model":"claude-3-7-sonnet-20250219","duration_seconds":0.151,"success":true,"tokens":{},"call_count":19},"pid":110158}
{"timestamp":"2025-06-25 17:54:29","session_id":"20250625_173119","level":"INFO","message":"Model response received successfully","context":{"provider":"anthropic","model":"claude-3-7-sonnet-20250219","response_length":25,"duration_seconds":0.151},"pid":110158}
{"timestamp":"2025-06-25 17:54:29","session_id":"20250625_173119","level":"INFO","message":"Discussion prediction for cluster 1","context":{"cluster_id":"1","event_type":"prediction","data":{"model":"claude-3-7-sonnet-20250219","round":1,"prediction":"Error: No valid responses"}},"pid":110158}
{"timestamp":"2025-06-25 17:54:29","session_id":"20250625_173119","level":"INFO","message":"Initialized openai processor","context":{"provider":"openai"},"pid":110158}
{"timestamp":"2025-06-25 17:54:29","session_id":"20250625_173119","level":"INFO","message":"Starting openai API request","context":{"model":"gpt-4o","provider":"openai"},"pid":110158} {"timestamp":"2025-06-25 17:54:30","session_id":"20250625_173119","level":"ERROR","message":"OpenAI API request failed","context":{"error":"You exceeded your current quota, please check your plan and billing details. For more information on this error, read the docs: https://platform.openai.com/docs/guides/error-codes/api-errors.","provider":"openai","model":"gpt-4o","status_code":429},"pid":110158}
{"timestamp":"2025-06-25 17:54:30","session_id":"20250625_173119","level":"ERROR","message":"Failed to process chunk 1: OpenAI API request failed: You exceeded your current quota, please check your plan and billing details. For more information on this error, read the docs: https://platform.openai.com/docs/guides/error-codes/api-errors.","context":{"provider":"openai","model":"gpt-4o","chunk":1,"error":"OpenAI API request failed: You exceeded your current quota, please check your plan and billing details. For more information on this error, read the docs: https://platform.openai.com/docs/guides/error-codes/api-errors."},"pid":110158} {"timestamp":"2025-06-25 17:54:30","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"openai","chunks_processed":1},"pid":110158} {"timestamp":"2025-06-25 17:54:30","session_id":"20250625_173119","level":"ERROR","message":"No valid responses received","context":{"provider":"openai","chunks_attempted":1},"pid":110158} {"timestamp":"2025-06-25 17:54:30","session_id":"20250625_173119","level":"INFO","message":"API call completed: openai/gpt-4o (0.828s)","context":{"provider":"openai","model":"gpt-4o","duration_seconds":0.828,"success":true,"tokens":{},"call_count":20},"pid":110158}
{"timestamp":"2025-06-25 17:54:30","session_id":"20250625_173119","level":"INFO","message":"API call completed: openai/gpt-4o (0.829s)","context":{"provider":"openai","model":"gpt-4o","duration_seconds":0.829,"success":true,"tokens":{},"call_count":21},"pid":110158}
{"timestamp":"2025-06-25 17:54:30","session_id":"20250625_173119","level":"INFO","message":"Model response received successfully","context":{"provider":"openai","model":"gpt-4o","response_length":25,"duration_seconds":0.829},"pid":110158}
{"timestamp":"2025-06-25 17:54:30","session_id":"20250625_173119","level":"INFO","message":"Discussion prediction for cluster 1","context":{"cluster_id":"1","event_type":"prediction","data":{"model":"gpt-4o","round":1,"prediction":"Error: No valid responses"}},"pid":110158}
{"timestamp":"2025-06-25 17:54:30","session_id":"20250625_173119","level":"WARN","message":"Model gemini-1.5-pro failed to provide valid response for cluster 1","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:54:30","session_id":"20250625_173119","level":"WARN","message":"Model grok-3-latest failed to provide valid response for cluster 1","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:54:30","session_id":"20250625_173119","level":"WARN","message":"Model claude-3-7-sonnet-20250219 failed to provide valid response for cluster 1","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:54:30","session_id":"20250625_173119","level":"WARN","message":"Model gpt-4o failed to provide valid response for cluster 1","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:54:30","session_id":"20250625_173119","level":"WARN","message":"Only 1 valid responses received for cluster 1. Skipping discussion.","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:54:30","session_id":"20250625_173119","level":"INFO","message":"Saved result to cache for cluster 1","context":{"cluster_id":"1"},"pid":110158}
{"timestamp":"2025-06-25 17:54:30","session_id":"20250625_173119","level":"INFO","message":"Completed discussion for cluster 1","context":{"cluster_id":"1"},"pid":110158} Completed discussion for cluster 1{"timestamp":"2025-06-25 17:54:30","session_id":"20250625_173119","level":"INFO","message":"Starting discussion for cluster 2...","context":{"cluster_id":"2"},"pid":110158}
Starting discussion for cluster 2...{"timestamp":"2025-06-25 17:54:30","session_id":"20250625_173119","level":"INFO","message":"Discussion start for cluster 2","context":{"cluster_id":"2","event_type":"start","data":{"tissue_name":"human blood CD4 T cells","marker_genes":"HLA-DQA2,EGFL6,TNFRSF4,SYT4,TIGIT,CA2,BACE2,KRT7,PHLDA2,HACD1"}},"pid":110158}
{"timestamp":"2025-06-25 17:54:30","session_id":"20250625_173119","level":"INFO","message":"Initialized gemini processor","context":{"provider":"gemini"},"pid":110158}
{"timestamp":"2025-06-25 17:54:30","session_id":"20250625_173119","level":"INFO","message":"Starting gemini API request","context":{"model":"gemini-2.0-flash","provider":"gemini"},"pid":110158}
{"timestamp":"2025-06-25 17:54:35","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"gemini","chunks_processed":1},"pid":110158}
{"timestamp":"2025-06-25 17:54:35","session_id":"20250625_173119","level":"INFO","message":"Results consolidated successfully","context":{"provider":"gemini","valid_chunks":1,"total_lines":14},"pid":110158}
{"timestamp":"2025-06-25 17:54:35","session_id":"20250625_173119","level":"INFO","message":"API call completed: gemini/gemini-2.0-flash (5.454s)","context":{"provider":"gemini","model":"gemini-2.0-flash","duration_seconds":5.454,"success":true,"tokens":{},"call_count":22},"pid":110158}
{"timestamp":"2025-06-25 17:54:35","session_id":"20250625_173119","level":"INFO","message":"API call completed: gemini/gemini-2.0-flash (5.456s)","context":{"provider":"gemini","model":"gemini-2.0-flash","duration_seconds":5.456,"success":true,"tokens":{},"call_count":23},"pid":110158}
{"timestamp":"2025-06-25 17:54:35","session_id":"20250625_173119","level":"INFO","message":"Model response received successfully","context":{"provider":"gemini","model":"gemini-2.0-flash","response_length":[26,0,210,0,776,0,8,303,148,149,0,521,0,640],"duration_seconds":5.456},"pid":110158}
{"timestamp":"2025-06-25 17:54:35","session_id":"20250625_173119","level":"INFO","message":"Discussion prediction for cluster 2","context":{"cluster_id":"2","event_type":"prediction","data":{"model":"gemini-2.0-flash","round":1,"prediction":["CELL TYPE: Likely Th2 cell","","GROUNDS: The gene expression profile of cluster 2 shows the presence of HLA-DQA2, EGFL6, TNFRSF4, SYT4, TIGIT, CA2, BACE2, KRT7, PHLDA2, and HACD1. Notably, TNFRSF4 (also known as OX40) and TIGIT are expressed.","","WARRANT: While no single marker is definitive, the presence of *TNFRSF4 (OX40)*, a co-stimulatory molecule strongly associated with activated T cells and, more specifically, Th2 differentiation and function in conjunction with TIGIT, points towards a Th2 phenotype. While not exclusively expressed in Th2 cells, OX40 is upregulated upon T cell activation, especially in Th2 responses. EGFL6 expression, while not a classical Th2 marker, may be associated with specific tissue contexts or activation states. Furthermore, KRT7 expression has been reported in some T cell subsets and might be indicative of particular activation stages or differentiation pathways. Other markers like HLA-DQA2 suggest MHC-II presentation capabilities, consistent with antigen-experienced T cells.","","BACKING:","* TNFRSF4 (OX40) has been extensively documented as a key regulator of Th2 responses. For example, targeting OX40 has been explored as a therapeutic approach to modulate allergic diseases driven by Th2 cells (e.g., Croft M. OX40 (CD134) and OX40L in T cell biology. *Annu Rev Immunol.* 2010;28:57-78).","* TIGIT can be expressed by many immune cell types, including T cells, but its co-expression with OX40 can further refine the potential cell type.","* The expression of genes like HLA-DQA2 is consistent with antigen-presenting capabilities which is consistent with the effector function of T cells.","","QUALIFIER: Probable. While the presence of TNFRSF4 is suggestive of a Th2 phenotype, the absence of more definitive Th2 markers (e.g., IL-4, IL-13, GATA3 at high levels) means this prediction is not definitive. The other genes listed may contribute to the overall cell state but are not specific indicators. Further analysis with cytokine staining or other functional assays would be necessary to confirm this prediction. The other markers could be associated with a different T cell activation state or tissue residency.","","REBUTTAL: Other models have given no prediction, indicating the limited specificity of these markers alone. The absence of other Th2-defining markers argues against a strong Th2 identity and suggests that these cells might represent an activated T cell population with some Th2 characteristics but not a fully committed Th2 cell. The expression profile might also represent a unique subset or transitional state of CD4 T cells and that more evidence would be needed to define the population accurately. Further single-cell RNA sequencing analysis with a larger panel of Th1, Th2, Th17, and Treg markers could better classify this cell type."]}},"pid":110158}
{"timestamp":"2025-06-25 17:54:35","session_id":"20250625_173119","level":"INFO","message":"Initialized gemini processor","context":{"provider":"gemini"},"pid":110158}
{"timestamp":"2025-06-25 17:54:35","session_id":"20250625_173119","level":"INFO","message":"Starting gemini API request","context":{"model":"gemini-1.5-pro","provider":"gemini"},"pid":110158} {"timestamp":"2025-06-25 17:54:35","session_id":"20250625_173119","level":"ERROR","message":"Gemini API request failed","context":{"error":"You exceeded your current quota, please check your plan and billing details. For more information on this error, head to: https://ai.google.dev/gemini-api/docs/rate-limits.","provider":"gemini","model":"gemini-1.5-pro","status_code":429},"pid":110158}
{"timestamp":"2025-06-25 17:54:35","session_id":"20250625_173119","level":"ERROR","message":"Failed to process chunk 1: Gemini API request failed: You exceeded your current quota, please check your plan and billing details. For more information on this error, head to: https://ai.google.dev/gemini-api/docs/rate-limits.","context":{"provider":"gemini","model":"gemini-1.5-pro","chunk":1,"error":"Gemini API request failed: You exceeded your current quota, please check your plan and billing details. For more information on this error, head to: https://ai.google.dev/gemini-api/docs/rate-limits."},"pid":110158} {"timestamp":"2025-06-25 17:54:35","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"gemini","chunks_processed":1},"pid":110158} {"timestamp":"2025-06-25 17:54:35","session_id":"20250625_173119","level":"ERROR","message":"No valid responses received","context":{"provider":"gemini","chunks_attempted":1},"pid":110158} {"timestamp":"2025-06-25 17:54:35","session_id":"20250625_173119","level":"INFO","message":"API call completed: gemini/gemini-1.5-pro (0.060s)","context":{"provider":"gemini","model":"gemini-1.5-pro","duration_seconds":0.06,"success":true,"tokens":{},"call_count":24},"pid":110158}
{"timestamp":"2025-06-25 17:54:35","session_id":"20250625_173119","level":"INFO","message":"API call completed: gemini/gemini-1.5-pro (0.062s)","context":{"provider":"gemini","model":"gemini-1.5-pro","duration_seconds":0.062,"success":true,"tokens":{},"call_count":25},"pid":110158}
{"timestamp":"2025-06-25 17:54:35","session_id":"20250625_173119","level":"INFO","message":"Model response received successfully","context":{"provider":"gemini","model":"gemini-1.5-pro","response_length":25,"duration_seconds":0.062},"pid":110158}
{"timestamp":"2025-06-25 17:54:35","session_id":"20250625_173119","level":"INFO","message":"Discussion prediction for cluster 2","context":{"cluster_id":"2","event_type":"prediction","data":{"model":"gemini-1.5-pro","round":1,"prediction":"Error: No valid responses"}},"pid":110158}
{"timestamp":"2025-06-25 17:54:35","session_id":"20250625_173119","level":"INFO","message":"Initialized grok processor","context":{"provider":"grok"},"pid":110158}
{"timestamp":"2025-06-25 17:54:35","session_id":"20250625_173119","level":"INFO","message":"Starting grok API request","context":{"model":"grok-3-latest","provider":"grok"},"pid":110158} {"timestamp":"2025-06-25 17:54:35","session_id":"20250625_173119","level":"ERROR","message":"Failed to process chunk 1: $ operator is invalid for atomic vectors","context":{"provider":"grok","model":"grok-3-latest","chunk":1,"error":"$ operator is invalid for atomic vectors"},"pid":110158} {"timestamp":"2025-06-25 17:54:35","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"grok","chunks_processed":1},"pid":110158} {"timestamp":"2025-06-25 17:54:35","session_id":"20250625_173119","level":"ERROR","message":"No valid responses received","context":{"provider":"grok","chunks_attempted":1},"pid":110158} {"timestamp":"2025-06-25 17:54:35","session_id":"20250625_173119","level":"INFO","message":"API call completed: grok/grok-3-latest (0.121s)","context":{"provider":"grok","model":"grok-3-latest","duration_seconds":0.121,"success":true,"tokens":{},"call_count":26},"pid":110158}
{"timestamp":"2025-06-25 17:54:35","session_id":"20250625_173119","level":"INFO","message":"API call completed: grok/grok-3-latest (0.123s)","context":{"provider":"grok","model":"grok-3-latest","duration_seconds":0.123,"success":true,"tokens":{},"call_count":27},"pid":110158}
{"timestamp":"2025-06-25 17:54:35","session_id":"20250625_173119","level":"INFO","message":"Model response received successfully","context":{"provider":"grok","model":"grok-3-latest","response_length":25,"duration_seconds":0.123},"pid":110158}
{"timestamp":"2025-06-25 17:54:35","session_id":"20250625_173119","level":"INFO","message":"Discussion prediction for cluster 2","context":{"cluster_id":"2","event_type":"prediction","data":{"model":"grok-3-latest","round":1,"prediction":"Error: No valid responses"}},"pid":110158}
{"timestamp":"2025-06-25 17:54:35","session_id":"20250625_173119","level":"INFO","message":"Initialized anthropic processor","context":{"provider":"anthropic"},"pid":110158}
{"timestamp":"2025-06-25 17:54:35","session_id":"20250625_173119","level":"INFO","message":"Starting anthropic API request","context":{"model":"claude-3-7-sonnet-20250219","provider":"anthropic"},"pid":110158} {"timestamp":"2025-06-25 17:54:36","session_id":"20250625_173119","level":"ERROR","message":"Anthropic API request failed","context":{"provider":"anthropic","model":"claude-3-7-sonnet-20250219","status_code":400,"error":"Your credit balance is too low to access the Anthropic API. Please go to Plans & Billing to upgrade or purchase credits."},"pid":110158}
{"timestamp":"2025-06-25 17:54:36","session_id":"20250625_173119","level":"ERROR","message":"Failed to process chunk 1: Anthropic API request failed: Your credit balance is too low to access the Anthropic API. Please go to Plans & Billing to upgrade or purchase credits.","context":{"provider":"anthropic","model":"claude-3-7-sonnet-20250219","chunk":1,"error":"Anthropic API request failed: Your credit balance is too low to access the Anthropic API. Please go to Plans & Billing to upgrade or purchase credits."},"pid":110158} {"timestamp":"2025-06-25 17:54:36","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"anthropic","chunks_processed":1},"pid":110158} {"timestamp":"2025-06-25 17:54:36","session_id":"20250625_173119","level":"ERROR","message":"No valid responses received","context":{"provider":"anthropic","chunks_attempted":1},"pid":110158} {"timestamp":"2025-06-25 17:54:36","session_id":"20250625_173119","level":"INFO","message":"API call completed: anthropic/claude-3-7-sonnet-20250219 (0.155s)","context":{"provider":"anthropic","model":"claude-3-7-sonnet-20250219","duration_seconds":0.155,"success":true,"tokens":{},"call_count":28},"pid":110158}
{"timestamp":"2025-06-25 17:54:36","session_id":"20250625_173119","level":"INFO","message":"API call completed: anthropic/claude-3-7-sonnet-20250219 (0.157s)","context":{"provider":"anthropic","model":"claude-3-7-sonnet-20250219","duration_seconds":0.157,"success":true,"tokens":{},"call_count":29},"pid":110158}
{"timestamp":"2025-06-25 17:54:36","session_id":"20250625_173119","level":"INFO","message":"Model response received successfully","context":{"provider":"anthropic","model":"claude-3-7-sonnet-20250219","response_length":25,"duration_seconds":0.157},"pid":110158}
{"timestamp":"2025-06-25 17:54:36","session_id":"20250625_173119","level":"INFO","message":"Discussion prediction for cluster 2","context":{"cluster_id":"2","event_type":"prediction","data":{"model":"claude-3-7-sonnet-20250219","round":1,"prediction":"Error: No valid responses"}},"pid":110158}
{"timestamp":"2025-06-25 17:54:36","session_id":"20250625_173119","level":"INFO","message":"Initialized openai processor","context":{"provider":"openai"},"pid":110158}
{"timestamp":"2025-06-25 17:54:36","session_id":"20250625_173119","level":"INFO","message":"Starting openai API request","context":{"model":"gpt-4o","provider":"openai"},"pid":110158} {"timestamp":"2025-06-25 17:54:36","session_id":"20250625_173119","level":"ERROR","message":"OpenAI API request failed","context":{"error":"You exceeded your current quota, please check your plan and billing details. For more information on this error, read the docs: https://platform.openai.com/docs/guides/error-codes/api-errors.","provider":"openai","model":"gpt-4o","status_code":429},"pid":110158}
{"timestamp":"2025-06-25 17:54:36","session_id":"20250625_173119","level":"ERROR","message":"Failed to process chunk 1: OpenAI API request failed: You exceeded your current quota, please check your plan and billing details. For more information on this error, read the docs: https://platform.openai.com/docs/guides/error-codes/api-errors.","context":{"provider":"openai","model":"gpt-4o","chunk":1,"error":"OpenAI API request failed: You exceeded your current quota, please check your plan and billing details. For more information on this error, read the docs: https://platform.openai.com/docs/guides/error-codes/api-errors."},"pid":110158} {"timestamp":"2025-06-25 17:54:36","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"openai","chunks_processed":1},"pid":110158} {"timestamp":"2025-06-25 17:54:36","session_id":"20250625_173119","level":"ERROR","message":"No valid responses received","context":{"provider":"openai","chunks_attempted":1},"pid":110158} {"timestamp":"2025-06-25 17:54:36","session_id":"20250625_173119","level":"INFO","message":"API call completed: openai/gpt-4o (0.455s)","context":{"provider":"openai","model":"gpt-4o","duration_seconds":0.455,"success":true,"tokens":{},"call_count":30},"pid":110158}
{"timestamp":"2025-06-25 17:54:36","session_id":"20250625_173119","level":"INFO","message":"API call completed: openai/gpt-4o (0.457s)","context":{"provider":"openai","model":"gpt-4o","duration_seconds":0.457,"success":true,"tokens":{},"call_count":31},"pid":110158}
{"timestamp":"2025-06-25 17:54:36","session_id":"20250625_173119","level":"INFO","message":"Model response received successfully","context":{"provider":"openai","model":"gpt-4o","response_length":25,"duration_seconds":0.457},"pid":110158}
{"timestamp":"2025-06-25 17:54:36","session_id":"20250625_173119","level":"INFO","message":"Discussion prediction for cluster 2","context":{"cluster_id":"2","event_type":"prediction","data":{"model":"gpt-4o","round":1,"prediction":"Error: No valid responses"}},"pid":110158}
{"timestamp":"2025-06-25 17:54:36","session_id":"20250625_173119","level":"WARN","message":"Model gemini-1.5-pro failed to provide valid response for cluster 2","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:54:36","session_id":"20250625_173119","level":"WARN","message":"Model grok-3-latest failed to provide valid response for cluster 2","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:54:36","session_id":"20250625_173119","level":"WARN","message":"Model claude-3-7-sonnet-20250219 failed to provide valid response for cluster 2","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:54:36","session_id":"20250625_173119","level":"WARN","message":"Model gpt-4o failed to provide valid response for cluster 2","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:54:36","session_id":"20250625_173119","level":"WARN","message":"Only 1 valid responses received for cluster 2. Skipping discussion.","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:54:36","session_id":"20250625_173119","level":"INFO","message":"Saved result to cache for cluster 2","context":{"cluster_id":"2"},"pid":110158}
{"timestamp":"2025-06-25 17:54:36","session_id":"20250625_173119","level":"INFO","message":"Completed discussion for cluster 2","context":{"cluster_id":"2"},"pid":110158} Completed discussion for cluster 2{"timestamp":"2025-06-25 17:54:36","session_id":"20250625_173119","level":"INFO","message":"Starting discussion for cluster 3...","context":{"cluster_id":"3"},"pid":110158}
Starting discussion for cluster 3...{"timestamp":"2025-06-25 17:54:36","session_id":"20250625_173119","level":"INFO","message":"Discussion start for cluster 3","context":{"cluster_id":"3","event_type":"start","data":{"tissue_name":"human blood CD4 T cells","marker_genes":"RPS4Y1,TCF7,LINC00861,SELL,GIMAP5,GIMAP7,GIMAP4,LEF1,PIK3IP1,FYB1"}},"pid":110158}
{"timestamp":"2025-06-25 17:54:36","session_id":"20250625_173119","level":"INFO","message":"Initialized gemini processor","context":{"provider":"gemini"},"pid":110158}
{"timestamp":"2025-06-25 17:54:36","session_id":"20250625_173119","level":"INFO","message":"Starting gemini API request","context":{"model":"gemini-2.0-flash","provider":"gemini"},"pid":110158}
{"timestamp":"2025-06-25 17:54:42","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"gemini","chunks_processed":1},"pid":110158}
{"timestamp":"2025-06-25 17:54:42","session_id":"20250625_173119","level":"INFO","message":"Results consolidated successfully","context":{"provider":"gemini","valid_chunks":1,"total_lines":16},"pid":110158}
{"timestamp":"2025-06-25 17:54:42","session_id":"20250625_173119","level":"INFO","message":"API call completed: gemini/gemini-2.0-flash (5.904s)","context":{"provider":"gemini","model":"gemini-2.0-flash","duration_seconds":5.904,"success":true,"tokens":{},"call_count":32},"pid":110158}
{"timestamp":"2025-06-25 17:54:42","session_id":"20250625_173119","level":"INFO","message":"API call completed: gemini/gemini-2.0-flash (5.906s)","context":{"provider":"gemini","model":"gemini-2.0-flash","duration_seconds":5.906,"success":true,"tokens":{},"call_count":33},"pid":110158}
{"timestamp":"2025-06-25 17:54:42","session_id":"20250625_173119","level":"INFO","message":"Model response received successfully","context":{"provider":"gemini","model":"gemini-2.0-flash","response_length":[33,0,118,0,656,0,8,223,284,240,154,73,0,289,0,688],"duration_seconds":5.906},"pid":110158}
{"timestamp":"2025-06-25 17:54:42","session_id":"20250625_173119","level":"INFO","message":"Discussion prediction for cluster 3","context":{"cluster_id":"3","event_type":"prediction","data":{"model":"gemini-2.0-flash","round":1,"prediction":["CELL TYPE: Naive Male CD4 T cells","","GROUNDS: The cluster expresses RPS4Y1, TCF7, LINC00861, SELL (CD62L), GIMAP5, GIMAP7, GIMAP4, LEF1, PIK3IP1, and FYB1.","","WARRANT: Expression of TCF7, LEF1, and SELL (CD62L) are indicative of naive T cells. GIMAP family members (GIMAP5, GIMAP7, GIMAP4) are also associated with T cell survival and homeostasis, and their expression is often observed in naive T cells. FYB1 is expressed in lymphocytes and is important for T cell signaling. The presence of RPS4Y1 indicates that the cells are from a male individual. LINC00861 and PIK3IP1, while less commonly cited as key markers, can also be expressed in T cells and do not contradict the naive T cell identity. The combination of these markers strongly suggests a naive CD4 T cell phenotype originating from a male individual.","","BACKING:","* TCF7 and LEF1 are transcription factors crucial for T cell development and maintenance of the naive state. (e.g., *Nature Immunology* reviews on T cell development). Their high expression is a hallmark of naive T cells.","* SELL (CD62L) is a cell adhesion molecule that allows T cells to home to secondary lymphoid organs. Its expression is high on naive T cells and is down-regulated upon activation. (e.g., SpringerBriefs in Immunology: Homing and Trafficking of Stem Cells and CD34+ Progenitor Cells).","* GIMAP family members play a role in T cell survival and apoptosis, and are highly expressed in quiescent, naive T cells. Studies on GIMAP function in T cells support this association (e.g., publications focusing on GIMAP gene families).","* FYB1 is an adapter protein involved in T cell receptor signaling, and its expression is expected in T cells (references on T cell signaling pathways).","* RPS4Y1 is a gene located on the Y chromosome, indicating male origin.","","QUALIFIER: Highly probable. The marker combination strongly supports the naive male CD4 T cell identity. However, without functional assays or further characterization (e.g., cytokine production upon stimulation, expression of other activation markers), complete certainty is not possible.","","REBUTTAL: Other models failed to provide a prediction, potentially due to a lack of training data encompassing all the marker genes simultaneously, or a higher threshold for assigning a cell type. While some of the genes are also expressed in other lymphocyte subsets, the specific combination presented here, particularly including TCF7, LEF1, SELL, and GIMAP family members, argues strongly against a more differentiated or activated T cell phenotype. The presence of RPS4Y1 unequivocally indicates the cluster is derived from a male individual. Therefore, although the models may have considered other possibilities, the weight of evidence leans heavily towards naive male CD4 T cells."]}},"pid":110158}
{"timestamp":"2025-06-25 17:54:42","session_id":"20250625_173119","level":"INFO","message":"Initialized gemini processor","context":{"provider":"gemini"},"pid":110158}
{"timestamp":"2025-06-25 17:54:42","session_id":"20250625_173119","level":"INFO","message":"Starting gemini API request","context":{"model":"gemini-1.5-pro","provider":"gemini"},"pid":110158} {"timestamp":"2025-06-25 17:54:42","session_id":"20250625_173119","level":"ERROR","message":"Gemini API request failed","context":{"error":"You exceeded your current quota, please check your plan and billing details. For more information on this error, head to: https://ai.google.dev/gemini-api/docs/rate-limits.","provider":"gemini","model":"gemini-1.5-pro","status_code":429},"pid":110158}
{"timestamp":"2025-06-25 17:54:42","session_id":"20250625_173119","level":"ERROR","message":"Failed to process chunk 1: Gemini API request failed: You exceeded your current quota, please check your plan and billing details. For more information on this error, head to: https://ai.google.dev/gemini-api/docs/rate-limits.","context":{"provider":"gemini","model":"gemini-1.5-pro","chunk":1,"error":"Gemini API request failed: You exceeded your current quota, please check your plan and billing details. For more information on this error, head to: https://ai.google.dev/gemini-api/docs/rate-limits."},"pid":110158} {"timestamp":"2025-06-25 17:54:42","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"gemini","chunks_processed":1},"pid":110158} {"timestamp":"2025-06-25 17:54:42","session_id":"20250625_173119","level":"ERROR","message":"No valid responses received","context":{"provider":"gemini","chunks_attempted":1},"pid":110158} {"timestamp":"2025-06-25 17:54:42","session_id":"20250625_173119","level":"INFO","message":"API call completed: gemini/gemini-1.5-pro (0.109s)","context":{"provider":"gemini","model":"gemini-1.5-pro","duration_seconds":0.109,"success":true,"tokens":{},"call_count":34},"pid":110158}
{"timestamp":"2025-06-25 17:54:42","session_id":"20250625_173119","level":"INFO","message":"API call completed: gemini/gemini-1.5-pro (0.111s)","context":{"provider":"gemini","model":"gemini-1.5-pro","duration_seconds":0.111,"success":true,"tokens":{},"call_count":35},"pid":110158}
{"timestamp":"2025-06-25 17:54:42","session_id":"20250625_173119","level":"INFO","message":"Model response received successfully","context":{"provider":"gemini","model":"gemini-1.5-pro","response_length":25,"duration_seconds":0.111},"pid":110158}
{"timestamp":"2025-06-25 17:54:42","session_id":"20250625_173119","level":"INFO","message":"Discussion prediction for cluster 3","context":{"cluster_id":"3","event_type":"prediction","data":{"model":"gemini-1.5-pro","round":1,"prediction":"Error: No valid responses"}},"pid":110158}
{"timestamp":"2025-06-25 17:54:42","session_id":"20250625_173119","level":"INFO","message":"Initialized grok processor","context":{"provider":"grok"},"pid":110158}
{"timestamp":"2025-06-25 17:54:42","session_id":"20250625_173119","level":"INFO","message":"Starting grok API request","context":{"model":"grok-3-latest","provider":"grok"},"pid":110158} {"timestamp":"2025-06-25 17:54:42","session_id":"20250625_173119","level":"ERROR","message":"Failed to process chunk 1: $ operator is invalid for atomic vectors","context":{"provider":"grok","model":"grok-3-latest","chunk":1,"error":"$ operator is invalid for atomic vectors"},"pid":110158} {"timestamp":"2025-06-25 17:54:42","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"grok","chunks_processed":1},"pid":110158} {"timestamp":"2025-06-25 17:54:42","session_id":"20250625_173119","level":"ERROR","message":"No valid responses received","context":{"provider":"grok","chunks_attempted":1},"pid":110158} {"timestamp":"2025-06-25 17:54:42","session_id":"20250625_173119","level":"INFO","message":"API call completed: grok/grok-3-latest (0.111s)","context":{"provider":"grok","model":"grok-3-latest","duration_seconds":0.111,"success":true,"tokens":{},"call_count":36},"pid":110158}
{"timestamp":"2025-06-25 17:54:42","session_id":"20250625_173119","level":"INFO","message":"API call completed: grok/grok-3-latest (0.113s)","context":{"provider":"grok","model":"grok-3-latest","duration_seconds":0.113,"success":true,"tokens":{},"call_count":37},"pid":110158}
{"timestamp":"2025-06-25 17:54:42","session_id":"20250625_173119","level":"INFO","message":"Model response received successfully","context":{"provider":"grok","model":"grok-3-latest","response_length":25,"duration_seconds":0.113},"pid":110158}
{"timestamp":"2025-06-25 17:54:42","session_id":"20250625_173119","level":"INFO","message":"Discussion prediction for cluster 3","context":{"cluster_id":"3","event_type":"prediction","data":{"model":"grok-3-latest","round":1,"prediction":"Error: No valid responses"}},"pid":110158}
{"timestamp":"2025-06-25 17:54:42","session_id":"20250625_173119","level":"INFO","message":"Initialized anthropic processor","context":{"provider":"anthropic"},"pid":110158}
{"timestamp":"2025-06-25 17:54:42","session_id":"20250625_173119","level":"INFO","message":"Starting anthropic API request","context":{"model":"claude-3-7-sonnet-20250219","provider":"anthropic"},"pid":110158} {"timestamp":"2025-06-25 17:54:42","session_id":"20250625_173119","level":"ERROR","message":"Anthropic API request failed","context":{"provider":"anthropic","model":"claude-3-7-sonnet-20250219","status_code":400,"error":"Your credit balance is too low to access the Anthropic API. Please go to Plans & Billing to upgrade or purchase credits."},"pid":110158}
{"timestamp":"2025-06-25 17:54:42","session_id":"20250625_173119","level":"ERROR","message":"Failed to process chunk 1: Anthropic API request failed: Your credit balance is too low to access the Anthropic API. Please go to Plans & Billing to upgrade or purchase credits.","context":{"provider":"anthropic","model":"claude-3-7-sonnet-20250219","chunk":1,"error":"Anthropic API request failed: Your credit balance is too low to access the Anthropic API. Please go to Plans & Billing to upgrade or purchase credits."},"pid":110158} {"timestamp":"2025-06-25 17:54:42","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"anthropic","chunks_processed":1},"pid":110158} {"timestamp":"2025-06-25 17:54:42","session_id":"20250625_173119","level":"ERROR","message":"No valid responses received","context":{"provider":"anthropic","chunks_attempted":1},"pid":110158} {"timestamp":"2025-06-25 17:54:42","session_id":"20250625_173119","level":"INFO","message":"API call completed: anthropic/claude-3-7-sonnet-20250219 (0.278s)","context":{"provider":"anthropic","model":"claude-3-7-sonnet-20250219","duration_seconds":0.278,"success":true,"tokens":{},"call_count":38},"pid":110158}
{"timestamp":"2025-06-25 17:54:42","session_id":"20250625_173119","level":"INFO","message":"API call completed: anthropic/claude-3-7-sonnet-20250219 (0.279s)","context":{"provider":"anthropic","model":"claude-3-7-sonnet-20250219","duration_seconds":0.279,"success":true,"tokens":{},"call_count":39},"pid":110158}
{"timestamp":"2025-06-25 17:54:42","session_id":"20250625_173119","level":"INFO","message":"Model response received successfully","context":{"provider":"anthropic","model":"claude-3-7-sonnet-20250219","response_length":25,"duration_seconds":0.279},"pid":110158}
{"timestamp":"2025-06-25 17:54:42","session_id":"20250625_173119","level":"INFO","message":"Discussion prediction for cluster 3","context":{"cluster_id":"3","event_type":"prediction","data":{"model":"claude-3-7-sonnet-20250219","round":1,"prediction":"Error: No valid responses"}},"pid":110158}
{"timestamp":"2025-06-25 17:54:42","session_id":"20250625_173119","level":"INFO","message":"Initialized openai processor","context":{"provider":"openai"},"pid":110158}
{"timestamp":"2025-06-25 17:54:42","session_id":"20250625_173119","level":"INFO","message":"Starting openai API request","context":{"model":"gpt-4o","provider":"openai"},"pid":110158} {"timestamp":"2025-06-25 17:54:43","session_id":"20250625_173119","level":"ERROR","message":"OpenAI API request failed","context":{"error":"You exceeded your current quota, please check your plan and billing details. For more information on this error, read the docs: https://platform.openai.com/docs/guides/error-codes/api-errors.","provider":"openai","model":"gpt-4o","status_code":429},"pid":110158}
{"timestamp":"2025-06-25 17:54:43","session_id":"20250625_173119","level":"ERROR","message":"Failed to process chunk 1: OpenAI API request failed: You exceeded your current quota, please check your plan and billing details. For more information on this error, read the docs: https://platform.openai.com/docs/guides/error-codes/api-errors.","context":{"provider":"openai","model":"gpt-4o","chunk":1,"error":"OpenAI API request failed: You exceeded your current quota, please check your plan and billing details. For more information on this error, read the docs: https://platform.openai.com/docs/guides/error-codes/api-errors."},"pid":110158} {"timestamp":"2025-06-25 17:54:43","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"openai","chunks_processed":1},"pid":110158} {"timestamp":"2025-06-25 17:54:43","session_id":"20250625_173119","level":"ERROR","message":"No valid responses received","context":{"provider":"openai","chunks_attempted":1},"pid":110158} {"timestamp":"2025-06-25 17:54:43","session_id":"20250625_173119","level":"INFO","message":"API call completed: openai/gpt-4o (0.170s)","context":{"provider":"openai","model":"gpt-4o","duration_seconds":0.17,"success":true,"tokens":{},"call_count":40},"pid":110158}
{"timestamp":"2025-06-25 17:54:43","session_id":"20250625_173119","level":"INFO","message":"API call completed: openai/gpt-4o (0.172s)","context":{"provider":"openai","model":"gpt-4o","duration_seconds":0.172,"success":true,"tokens":{},"call_count":41},"pid":110158}
{"timestamp":"2025-06-25 17:54:43","session_id":"20250625_173119","level":"INFO","message":"Model response received successfully","context":{"provider":"openai","model":"gpt-4o","response_length":25,"duration_seconds":0.172},"pid":110158}
{"timestamp":"2025-06-25 17:54:43","session_id":"20250625_173119","level":"INFO","message":"Discussion prediction for cluster 3","context":{"cluster_id":"3","event_type":"prediction","data":{"model":"gpt-4o","round":1,"prediction":"Error: No valid responses"}},"pid":110158}
{"timestamp":"2025-06-25 17:54:43","session_id":"20250625_173119","level":"WARN","message":"Model gemini-1.5-pro failed to provide valid response for cluster 3","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:54:43","session_id":"20250625_173119","level":"WARN","message":"Model grok-3-latest failed to provide valid response for cluster 3","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:54:43","session_id":"20250625_173119","level":"WARN","message":"Model claude-3-7-sonnet-20250219 failed to provide valid response for cluster 3","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:54:43","session_id":"20250625_173119","level":"WARN","message":"Model gpt-4o failed to provide valid response for cluster 3","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:54:43","session_id":"20250625_173119","level":"WARN","message":"Only 1 valid responses received for cluster 3. Skipping discussion.","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:54:43","session_id":"20250625_173119","level":"INFO","message":"Saved result to cache for cluster 3","context":{"cluster_id":"3"},"pid":110158}
{"timestamp":"2025-06-25 17:54:43","session_id":"20250625_173119","level":"INFO","message":"Completed discussion for cluster 3","context":{"cluster_id":"3"},"pid":110158} Completed discussion for cluster 3{"timestamp":"2025-06-25 17:54:43","session_id":"20250625_173119","level":"INFO","message":"Starting discussion for cluster 4...","context":{"cluster_id":"4"},"pid":110158}
Starting discussion for cluster 4...{"timestamp":"2025-06-25 17:54:43","session_id":"20250625_173119","level":"INFO","message":"Discussion start for cluster 4","context":{"cluster_id":"4","event_type":"start","data":{"tissue_name":"human blood CD4 T cells","marker_genes":"PPBP,FCER2,DNAJC12,SLC7A11-AS1,CSMD1,BLVRB,CDKN2A,PPP2R2B,PAGE5,C1orf162"}},"pid":110158}
{"timestamp":"2025-06-25 17:54:43","session_id":"20250625_173119","level":"INFO","message":"Initialized gemini processor","context":{"provider":"gemini"},"pid":110158}
{"timestamp":"2025-06-25 17:54:43","session_id":"20250625_173119","level":"INFO","message":"Starting gemini API request","context":{"model":"gemini-2.0-flash","provider":"gemini"},"pid":110158}
{"timestamp":"2025-06-25 17:54:48","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"gemini","chunks_processed":1},"pid":110158}
{"timestamp":"2025-06-25 17:54:48","session_id":"20250625_173119","level":"INFO","message":"Results consolidated successfully","context":{"provider":"gemini","valid_chunks":1,"total_lines":14},"pid":110158}
{"timestamp":"2025-06-25 17:54:48","session_id":"20250625_173119","level":"INFO","message":"API call completed: gemini/gemini-2.0-flash (5.682s)","context":{"provider":"gemini","model":"gemini-2.0-flash","duration_seconds":5.682,"success":true,"tokens":{},"call_count":42},"pid":110158}
{"timestamp":"2025-06-25 17:54:48","session_id":"20250625_173119","level":"INFO","message":"API call completed: gemini/gemini-2.0-flash (5.684s)","context":{"provider":"gemini","model":"gemini-2.0-flash","duration_seconds":5.684,"success":true,"tokens":{},"call_count":43},"pid":110158}
{"timestamp":"2025-06-25 17:54:48","session_id":"20250625_173119","level":"INFO","message":"Model response received successfully","context":{"provider":"gemini","model":"gemini-2.0-flash","response_length":[61,0,701,0,451,0,8,217,209,221,0,339,0,622],"duration_seconds":5.684},"pid":110158}
{"timestamp":"2025-06-25 17:54:48","session_id":"20250625_173119","level":"INFO","message":"Discussion prediction for cluster 4","context":{"cluster_id":"4","event_type":"prediction","data":{"model":"gemini-2.0-flash","round":1,"prediction":["CELL TYPE: Megakaryocyte or Platelet Contaminated CD4 T Cells","","GROUNDS: The marker genes expressed in this cluster are PPBP, FCER2, DNAJC12, SLC7A11-AS1, CSMD1, BLVRB, CDKN2A, PPP2R2B, PAGE5, and C1orf162. Notably, PPBP (Pro-Platelet Basic Protein, also known as CXCL7) is a strong indicator of megakaryocytes or platelets, and FCER2 (CD23) can also be expressed on platelets. While some markers like CDKN2A and CSMD1 are expressed across various cell types, their presence combined with PPBP and FCER2 suggests a stronger link to platelet contamination. The presence of SLC7A11-AS1 is less specific but can be seen in various cancer types. Markers like DNAJC12, BLVRB, PPP2R2B, PAGE5 and C1orf162 don't provide immediately clear specific cell type identification.","","WARRANT: The presence of PPBP, a chemokine released by platelets, is highly indicative of either megakaryocytes or platelet contamination in the CD4 T cell sample. While some of the other listed genes can be expressed in CD4 T cells, the co-expression of PPBP and FCER2 points towards a significant platelet contribution to the gene expression profile of this cluster. The remaining genes lack the specificity to definitively overturn this indication.","","BACKING:","* PPBP is a well-established marker for megakaryocytes and platelets. Its presence is routinely used to identify these cells in various studies. (e.g., search for PPBP in single-cell RNA sequencing studies of blood)","* FCER2 (CD23) can be expressed on both B cells and platelets, although its expression on B cells is more commonly associated with immune regulation. (e.g., research articles on CD23 expression on platelets)","* Single-cell RNA sequencing studies often report platelet contamination as a common issue, especially when working with unsorted blood samples. It's common to find platelet markers in other cell types due to adherence.","","QUALIFIER: Highly probable. While it's possible that the CD4 T cells in this cluster are expressing PPBP at a low level, the more likely scenario is contamination with platelets or megakaryocyte fragments. Further investigation, such as flow cytometry analysis with platelet-specific markers alongside CD4, would be needed to confirm this.","","REBUTTAL: Other models returned \"No prediction\" or \"Unknown\". This highlights the difficulty in accurately identifying cell types solely based on a limited gene list. The absence of canonical CD4 T cell marker genes (e.g., CD3, CD4, CCR7) further supports the argument against this cluster being pure CD4 T cells. While genes like CDKN2A may be expressed in T cells, their presence alongside PPBP and FCER2 shifts the probability towards platelet contamination. Therefore, while CD4 T cells may be present, their signal is likely overwhelmed by the expression profile driven by the presence of platelets or megakaryocytes."]}},"pid":110158}
{"timestamp":"2025-06-25 17:54:48","session_id":"20250625_173119","level":"INFO","message":"Initialized gemini processor","context":{"provider":"gemini"},"pid":110158}
{"timestamp":"2025-06-25 17:54:48","session_id":"20250625_173119","level":"INFO","message":"Starting gemini API request","context":{"model":"gemini-1.5-pro","provider":"gemini"},"pid":110158} {"timestamp":"2025-06-25 17:54:48","session_id":"20250625_173119","level":"ERROR","message":"Gemini API request failed","context":{"error":"You exceeded your current quota, please check your plan and billing details. For more information on this error, head to: https://ai.google.dev/gemini-api/docs/rate-limits.","provider":"gemini","model":"gemini-1.5-pro","status_code":429},"pid":110158}
{"timestamp":"2025-06-25 17:54:48","session_id":"20250625_173119","level":"ERROR","message":"Failed to process chunk 1: Gemini API request failed: You exceeded your current quota, please check your plan and billing details. For more information on this error, head to: https://ai.google.dev/gemini-api/docs/rate-limits.","context":{"provider":"gemini","model":"gemini-1.5-pro","chunk":1,"error":"Gemini API request failed: You exceeded your current quota, please check your plan and billing details. For more information on this error, head to: https://ai.google.dev/gemini-api/docs/rate-limits."},"pid":110158} {"timestamp":"2025-06-25 17:54:48","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"gemini","chunks_processed":1},"pid":110158} {"timestamp":"2025-06-25 17:54:48","session_id":"20250625_173119","level":"ERROR","message":"No valid responses received","context":{"provider":"gemini","chunks_attempted":1},"pid":110158} {"timestamp":"2025-06-25 17:54:48","session_id":"20250625_173119","level":"INFO","message":"API call completed: gemini/gemini-1.5-pro (0.070s)","context":{"provider":"gemini","model":"gemini-1.5-pro","duration_seconds":0.07,"success":true,"tokens":{},"call_count":44},"pid":110158}
{"timestamp":"2025-06-25 17:54:48","session_id":"20250625_173119","level":"INFO","message":"API call completed: gemini/gemini-1.5-pro (0.072s)","context":{"provider":"gemini","model":"gemini-1.5-pro","duration_seconds":0.072,"success":true,"tokens":{},"call_count":45},"pid":110158}
{"timestamp":"2025-06-25 17:54:48","session_id":"20250625_173119","level":"INFO","message":"Model response received successfully","context":{"provider":"gemini","model":"gemini-1.5-pro","response_length":25,"duration_seconds":0.072},"pid":110158}
{"timestamp":"2025-06-25 17:54:48","session_id":"20250625_173119","level":"INFO","message":"Discussion prediction for cluster 4","context":{"cluster_id":"4","event_type":"prediction","data":{"model":"gemini-1.5-pro","round":1,"prediction":"Error: No valid responses"}},"pid":110158}
{"timestamp":"2025-06-25 17:54:48","session_id":"20250625_173119","level":"INFO","message":"Initialized grok processor","context":{"provider":"grok"},"pid":110158}
{"timestamp":"2025-06-25 17:54:48","session_id":"20250625_173119","level":"INFO","message":"Starting grok API request","context":{"model":"grok-3-latest","provider":"grok"},"pid":110158} {"timestamp":"2025-06-25 17:54:49","session_id":"20250625_173119","level":"ERROR","message":"Failed to process chunk 1: $ operator is invalid for atomic vectors","context":{"provider":"grok","model":"grok-3-latest","chunk":1,"error":"$ operator is invalid for atomic vectors"},"pid":110158} {"timestamp":"2025-06-25 17:54:49","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"grok","chunks_processed":1},"pid":110158} {"timestamp":"2025-06-25 17:54:49","session_id":"20250625_173119","level":"ERROR","message":"No valid responses received","context":{"provider":"grok","chunks_attempted":1},"pid":110158} {"timestamp":"2025-06-25 17:54:49","session_id":"20250625_173119","level":"INFO","message":"API call completed: grok/grok-3-latest (0.124s)","context":{"provider":"grok","model":"grok-3-latest","duration_seconds":0.124,"success":true,"tokens":{},"call_count":46},"pid":110158}
{"timestamp":"2025-06-25 17:54:49","session_id":"20250625_173119","level":"INFO","message":"API call completed: grok/grok-3-latest (0.125s)","context":{"provider":"grok","model":"grok-3-latest","duration_seconds":0.125,"success":true,"tokens":{},"call_count":47},"pid":110158}
{"timestamp":"2025-06-25 17:54:49","session_id":"20250625_173119","level":"INFO","message":"Model response received successfully","context":{"provider":"grok","model":"grok-3-latest","response_length":25,"duration_seconds":0.125},"pid":110158}
{"timestamp":"2025-06-25 17:54:49","session_id":"20250625_173119","level":"INFO","message":"Discussion prediction for cluster 4","context":{"cluster_id":"4","event_type":"prediction","data":{"model":"grok-3-latest","round":1,"prediction":"Error: No valid responses"}},"pid":110158}
{"timestamp":"2025-06-25 17:54:49","session_id":"20250625_173119","level":"INFO","message":"Initialized anthropic processor","context":{"provider":"anthropic"},"pid":110158}
{"timestamp":"2025-06-25 17:54:49","session_id":"20250625_173119","level":"INFO","message":"Starting anthropic API request","context":{"model":"claude-3-7-sonnet-20250219","provider":"anthropic"},"pid":110158} {"timestamp":"2025-06-25 17:54:49","session_id":"20250625_173119","level":"ERROR","message":"Anthropic API request failed","context":{"provider":"anthropic","model":"claude-3-7-sonnet-20250219","status_code":400,"error":"Your credit balance is too low to access the Anthropic API. Please go to Plans & Billing to upgrade or purchase credits."},"pid":110158}
{"timestamp":"2025-06-25 17:54:49","session_id":"20250625_173119","level":"ERROR","message":"Failed to process chunk 1: Anthropic API request failed: Your credit balance is too low to access the Anthropic API. Please go to Plans & Billing to upgrade or purchase credits.","context":{"provider":"anthropic","model":"claude-3-7-sonnet-20250219","chunk":1,"error":"Anthropic API request failed: Your credit balance is too low to access the Anthropic API. Please go to Plans & Billing to upgrade or purchase credits."},"pid":110158} {"timestamp":"2025-06-25 17:54:49","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"anthropic","chunks_processed":1},"pid":110158} {"timestamp":"2025-06-25 17:54:49","session_id":"20250625_173119","level":"ERROR","message":"No valid responses received","context":{"provider":"anthropic","chunks_attempted":1},"pid":110158} {"timestamp":"2025-06-25 17:54:49","session_id":"20250625_173119","level":"INFO","message":"API call completed: anthropic/claude-3-7-sonnet-20250219 (0.250s)","context":{"provider":"anthropic","model":"claude-3-7-sonnet-20250219","duration_seconds":0.25,"success":true,"tokens":{},"call_count":48},"pid":110158}
{"timestamp":"2025-06-25 17:54:49","session_id":"20250625_173119","level":"INFO","message":"API call completed: anthropic/claude-3-7-sonnet-20250219 (0.251s)","context":{"provider":"anthropic","model":"claude-3-7-sonnet-20250219","duration_seconds":0.251,"success":true,"tokens":{},"call_count":49},"pid":110158}
{"timestamp":"2025-06-25 17:54:49","session_id":"20250625_173119","level":"INFO","message":"Model response received successfully","context":{"provider":"anthropic","model":"claude-3-7-sonnet-20250219","response_length":25,"duration_seconds":0.251},"pid":110158}
{"timestamp":"2025-06-25 17:54:49","session_id":"20250625_173119","level":"INFO","message":"Discussion prediction for cluster 4","context":{"cluster_id":"4","event_type":"prediction","data":{"model":"claude-3-7-sonnet-20250219","round":1,"prediction":"Error: No valid responses"}},"pid":110158}
{"timestamp":"2025-06-25 17:54:49","session_id":"20250625_173119","level":"INFO","message":"Initialized openai processor","context":{"provider":"openai"},"pid":110158}
{"timestamp":"2025-06-25 17:54:49","session_id":"20250625_173119","level":"INFO","message":"Starting openai API request","context":{"model":"gpt-4o","provider":"openai"},"pid":110158} {"timestamp":"2025-06-25 17:54:49","session_id":"20250625_173119","level":"ERROR","message":"OpenAI API request failed","context":{"error":"You exceeded your current quota, please check your plan and billing details. For more information on this error, read the docs: https://platform.openai.com/docs/guides/error-codes/api-errors.","provider":"openai","model":"gpt-4o","status_code":429},"pid":110158}
{"timestamp":"2025-06-25 17:54:49","session_id":"20250625_173119","level":"ERROR","message":"Failed to process chunk 1: OpenAI API request failed: You exceeded your current quota, please check your plan and billing details. For more information on this error, read the docs: https://platform.openai.com/docs/guides/error-codes/api-errors.","context":{"provider":"openai","model":"gpt-4o","chunk":1,"error":"OpenAI API request failed: You exceeded your current quota, please check your plan and billing details. For more information on this error, read the docs: https://platform.openai.com/docs/guides/error-codes/api-errors."},"pid":110158} {"timestamp":"2025-06-25 17:54:49","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"openai","chunks_processed":1},"pid":110158} {"timestamp":"2025-06-25 17:54:49","session_id":"20250625_173119","level":"ERROR","message":"No valid responses received","context":{"provider":"openai","chunks_attempted":1},"pid":110158} {"timestamp":"2025-06-25 17:54:49","session_id":"20250625_173119","level":"INFO","message":"API call completed: openai/gpt-4o (0.642s)","context":{"provider":"openai","model":"gpt-4o","duration_seconds":0.642,"success":true,"tokens":{},"call_count":50},"pid":110158}
{"timestamp":"2025-06-25 17:54:49","session_id":"20250625_173119","level":"INFO","message":"API call completed: openai/gpt-4o (0.643s)","context":{"provider":"openai","model":"gpt-4o","duration_seconds":0.643,"success":true,"tokens":{},"call_count":51},"pid":110158}
{"timestamp":"2025-06-25 17:54:49","session_id":"20250625_173119","level":"INFO","message":"Model response received successfully","context":{"provider":"openai","model":"gpt-4o","response_length":25,"duration_seconds":0.643},"pid":110158}
{"timestamp":"2025-06-25 17:54:49","session_id":"20250625_173119","level":"INFO","message":"Discussion prediction for cluster 4","context":{"cluster_id":"4","event_type":"prediction","data":{"model":"gpt-4o","round":1,"prediction":"Error: No valid responses"}},"pid":110158}
{"timestamp":"2025-06-25 17:54:49","session_id":"20250625_173119","level":"WARN","message":"Model gemini-1.5-pro failed to provide valid response for cluster 4","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:54:49","session_id":"20250625_173119","level":"WARN","message":"Model grok-3-latest failed to provide valid response for cluster 4","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:54:49","session_id":"20250625_173119","level":"WARN","message":"Model claude-3-7-sonnet-20250219 failed to provide valid response for cluster 4","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:54:49","session_id":"20250625_173119","level":"WARN","message":"Model gpt-4o failed to provide valid response for cluster 4","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:54:49","session_id":"20250625_173119","level":"WARN","message":"Only 1 valid responses received for cluster 4. Skipping discussion.","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:54:49","session_id":"20250625_173119","level":"INFO","message":"Saved result to cache for cluster 4","context":{"cluster_id":"4"},"pid":110158}
{"timestamp":"2025-06-25 17:54:49","session_id":"20250625_173119","level":"INFO","message":"Completed discussion for cluster 4","context":{"cluster_id":"4"},"pid":110158} Completed discussion for cluster 4{"timestamp":"2025-06-25 17:54:49","session_id":"20250625_173119","level":"INFO","message":"Starting discussion for cluster 5...","context":{"cluster_id":"5"},"pid":110158}
Starting discussion for cluster 5...{"timestamp":"2025-06-25 17:54:49","session_id":"20250625_173119","level":"INFO","message":"Discussion start for cluster 5","context":{"cluster_id":"5","event_type":"start","data":{"tissue_name":"human blood CD4 T cells","marker_genes":"TTC29,KRT1,LINC02752,TBX4,PLCB1,AC069410.1,SP5,TNS4,TRAV38-2DV8,IL4"}},"pid":110158}
{"timestamp":"2025-06-25 17:54:49","session_id":"20250625_173119","level":"INFO","message":"Initialized gemini processor","context":{"provider":"gemini"},"pid":110158}
{"timestamp":"2025-06-25 17:54:49","session_id":"20250625_173119","level":"INFO","message":"Starting gemini API request","context":{"model":"gemini-2.0-flash","provider":"gemini"},"pid":110158}
{"timestamp":"2025-06-25 17:54:54","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"gemini","chunks_processed":1},"pid":110158}
{"timestamp":"2025-06-25 17:54:54","session_id":"20250625_173119","level":"INFO","message":"Results consolidated successfully","context":{"provider":"gemini","valid_chunks":1,"total_lines":16},"pid":110158}
{"timestamp":"2025-06-25 17:54:54","session_id":"20250625_173119","level":"INFO","message":"API call completed: gemini/gemini-2.0-flash (5.015s)","context":{"provider":"gemini","model":"gemini-2.0-flash","duration_seconds":5.015,"success":true,"tokens":{},"call_count":52},"pid":110158}
{"timestamp":"2025-06-25 17:54:54","session_id":"20250625_173119","level":"INFO","message":"API call completed: gemini/gemini-2.0-flash (5.017s)","context":{"provider":"gemini","model":"gemini-2.0-flash","duration_seconds":5.017,"success":true,"tokens":{},"call_count":53},"pid":110158}
{"timestamp":"2025-06-25 17:54:54","session_id":"20250625_173119","level":"INFO","message":"Model response received successfully","context":{"provider":"gemini","model":"gemini-2.0-flash","response_length":[51,0,78,0,791,0,8,172,128,122,163,135,0,314,0,846],"duration_seconds":5.017},"pid":110158}
{"timestamp":"2025-06-25 17:54:54","session_id":"20250625_173119","level":"INFO","message":"Discussion prediction for cluster 5","context":{"cluster_id":"5","event_type":"prediction","data":{"model":"gemini-2.0-flash","round":1,"prediction":["CELL TYPE: CD4+ Helper T cell, likely a Th2 subset.","","GROUNDS: The cluster expresses the marker genes *TBX4, IL4, PLCB1, SP5, TNS4*.","","WARRANT: *TBX4* is a transcription factor with known roles in immune cell differentiation, including T cell lineage specification. *IL4* is a signature cytokine produced by Th2 cells and is critical for their function in promoting humoral immunity against extracellular parasites and allergens. *PLCB1* (Phospholipase C Beta 1) is involved in TCR signaling, essential for T cell activation. *SP5* is a transcription factor involved in development and differentiation and has been shown to be expressed in T cells. *TNS4* (Tensin 4) is involved in cell adhesion and migration, processes relevant to T cell function. While *TTC29*, *KRT1*, *LINC02752*, *AC069410.1*, and *TRAV38-2DV8* are present, their significance in identifying specific T cell subtypes is less established or more general.","","BACKING:","* The Immunological Genome Project (ImmGen) database is a comprehensive resource for gene expression in immune cells and supports the association of *IL4* with Th2 cells.","* Literature on Th2 differentiation pathways highlights *IL4* as a key cytokine driver (e.g., PMID: 24275567, PMID: 15680327).","* Studies on TCR signaling in T cells demonstrate the importance of *PLCB1* in T cell activation (e.g., PMID: 28636583).","* Expression databases (e.g., Gene Expression Omnibus (GEO)) can be queried to validate the co-expression of these genes in CD4+ T cells, particularly Th2 cells.","* The roles of SP5 and TNS4, while not as directly indicative, support broader T cell functions (e.g., PMID: 15760857, PMID: 28719263).","","QUALIFIER: Probable. While *IL4* strongly suggests a Th2 phenotype, confirmation with additional markers (e.g., GATA3, STAT6) and functional assays (e.g., cytokine secretion) would increase certainty. The presence of *TBX4, PLCB1, SP5 and TNS4* further strengthens the case for a T cell lineage, specifically CD4+.","","REBUTTAL: The lack of prediction from other models could be due to several factors: 1) incomplete training data for these specific gene combinations, 2) different weighting of gene importance in their algorithms, or 3) the ambiguous nature of some of the markers in defining precise cell subtypes. *TTC29, KRT1, LINC02752, AC069410.1, and TRAV38-2DV8* are less specific markers and could potentially mislead models if interpreted incorrectly. *KRT1*, for instance, is typically associated with epithelial cells, so its presence here could indicate contamination, although more recent studies show it can also be expressed in immune cells. Therefore, a more comprehensive investigation considering a broader panel of genes is recommended. However, the strong presence of *IL4* overrides these concerns and leans heavily towards Th2 identification."]}},"pid":110158}
{"timestamp":"2025-06-25 17:54:54","session_id":"20250625_173119","level":"INFO","message":"Initialized gemini processor","context":{"provider":"gemini"},"pid":110158}
{"timestamp":"2025-06-25 17:54:54","session_id":"20250625_173119","level":"INFO","message":"Starting gemini API request","context":{"model":"gemini-1.5-pro","provider":"gemini"},"pid":110158} {"timestamp":"2025-06-25 17:54:55","session_id":"20250625_173119","level":"ERROR","message":"Gemini API request failed","context":{"error":"You exceeded your current quota, please check your plan and billing details. For more information on this error, head to: https://ai.google.dev/gemini-api/docs/rate-limits.","provider":"gemini","model":"gemini-1.5-pro","status_code":429},"pid":110158}
{"timestamp":"2025-06-25 17:54:55","session_id":"20250625_173119","level":"ERROR","message":"Failed to process chunk 1: Gemini API request failed: You exceeded your current quota, please check your plan and billing details. For more information on this error, head to: https://ai.google.dev/gemini-api/docs/rate-limits.","context":{"provider":"gemini","model":"gemini-1.5-pro","chunk":1,"error":"Gemini API request failed: You exceeded your current quota, please check your plan and billing details. For more information on this error, head to: https://ai.google.dev/gemini-api/docs/rate-limits."},"pid":110158} {"timestamp":"2025-06-25 17:54:55","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"gemini","chunks_processed":1},"pid":110158} {"timestamp":"2025-06-25 17:54:55","session_id":"20250625_173119","level":"ERROR","message":"No valid responses received","context":{"provider":"gemini","chunks_attempted":1},"pid":110158} {"timestamp":"2025-06-25 17:54:55","session_id":"20250625_173119","level":"INFO","message":"API call completed: gemini/gemini-1.5-pro (0.067s)","context":{"provider":"gemini","model":"gemini-1.5-pro","duration_seconds":0.067,"success":true,"tokens":{},"call_count":54},"pid":110158}
{"timestamp":"2025-06-25 17:54:55","session_id":"20250625_173119","level":"INFO","message":"API call completed: gemini/gemini-1.5-pro (0.069s)","context":{"provider":"gemini","model":"gemini-1.5-pro","duration_seconds":0.069,"success":true,"tokens":{},"call_count":55},"pid":110158}
{"timestamp":"2025-06-25 17:54:55","session_id":"20250625_173119","level":"INFO","message":"Model response received successfully","context":{"provider":"gemini","model":"gemini-1.5-pro","response_length":25,"duration_seconds":0.069},"pid":110158}
{"timestamp":"2025-06-25 17:54:55","session_id":"20250625_173119","level":"INFO","message":"Discussion prediction for cluster 5","context":{"cluster_id":"5","event_type":"prediction","data":{"model":"gemini-1.5-pro","round":1,"prediction":"Error: No valid responses"}},"pid":110158}
{"timestamp":"2025-06-25 17:54:55","session_id":"20250625_173119","level":"INFO","message":"Initialized grok processor","context":{"provider":"grok"},"pid":110158}
{"timestamp":"2025-06-25 17:54:55","session_id":"20250625_173119","level":"INFO","message":"Starting grok API request","context":{"model":"grok-3-latest","provider":"grok"},"pid":110158} {"timestamp":"2025-06-25 17:54:55","session_id":"20250625_173119","level":"ERROR","message":"Failed to process chunk 1: $ operator is invalid for atomic vectors","context":{"provider":"grok","model":"grok-3-latest","chunk":1,"error":"$ operator is invalid for atomic vectors"},"pid":110158} {"timestamp":"2025-06-25 17:54:55","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"grok","chunks_processed":1},"pid":110158} {"timestamp":"2025-06-25 17:54:55","session_id":"20250625_173119","level":"ERROR","message":"No valid responses received","context":{"provider":"grok","chunks_attempted":1},"pid":110158} {"timestamp":"2025-06-25 17:54:55","session_id":"20250625_173119","level":"INFO","message":"API call completed: grok/grok-3-latest (0.113s)","context":{"provider":"grok","model":"grok-3-latest","duration_seconds":0.113,"success":true,"tokens":{},"call_count":56},"pid":110158}
{"timestamp":"2025-06-25 17:54:55","session_id":"20250625_173119","level":"INFO","message":"API call completed: grok/grok-3-latest (0.114s)","context":{"provider":"grok","model":"grok-3-latest","duration_seconds":0.114,"success":true,"tokens":{},"call_count":57},"pid":110158}
{"timestamp":"2025-06-25 17:54:55","session_id":"20250625_173119","level":"INFO","message":"Model response received successfully","context":{"provider":"grok","model":"grok-3-latest","response_length":25,"duration_seconds":0.114},"pid":110158}
{"timestamp":"2025-06-25 17:54:55","session_id":"20250625_173119","level":"INFO","message":"Discussion prediction for cluster 5","context":{"cluster_id":"5","event_type":"prediction","data":{"model":"grok-3-latest","round":1,"prediction":"Error: No valid responses"}},"pid":110158}
{"timestamp":"2025-06-25 17:54:55","session_id":"20250625_173119","level":"INFO","message":"Initialized anthropic processor","context":{"provider":"anthropic"},"pid":110158}
{"timestamp":"2025-06-25 17:54:55","session_id":"20250625_173119","level":"INFO","message":"Starting anthropic API request","context":{"model":"claude-3-7-sonnet-20250219","provider":"anthropic"},"pid":110158} {"timestamp":"2025-06-25 17:54:55","session_id":"20250625_173119","level":"ERROR","message":"Anthropic API request failed","context":{"provider":"anthropic","model":"claude-3-7-sonnet-20250219","status_code":400,"error":"Your credit balance is too low to access the Anthropic API. Please go to Plans & Billing to upgrade or purchase credits."},"pid":110158}
{"timestamp":"2025-06-25 17:54:55","session_id":"20250625_173119","level":"ERROR","message":"Failed to process chunk 1: Anthropic API request failed: Your credit balance is too low to access the Anthropic API. Please go to Plans & Billing to upgrade or purchase credits.","context":{"provider":"anthropic","model":"claude-3-7-sonnet-20250219","chunk":1,"error":"Anthropic API request failed: Your credit balance is too low to access the Anthropic API. Please go to Plans & Billing to upgrade or purchase credits."},"pid":110158} {"timestamp":"2025-06-25 17:54:55","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"anthropic","chunks_processed":1},"pid":110158} {"timestamp":"2025-06-25 17:54:55","session_id":"20250625_173119","level":"ERROR","message":"No valid responses received","context":{"provider":"anthropic","chunks_attempted":1},"pid":110158} {"timestamp":"2025-06-25 17:54:55","session_id":"20250625_173119","level":"INFO","message":"API call completed: anthropic/claude-3-7-sonnet-20250219 (0.143s)","context":{"provider":"anthropic","model":"claude-3-7-sonnet-20250219","duration_seconds":0.143,"success":true,"tokens":{},"call_count":58},"pid":110158}
{"timestamp":"2025-06-25 17:54:55","session_id":"20250625_173119","level":"INFO","message":"API call completed: anthropic/claude-3-7-sonnet-20250219 (0.144s)","context":{"provider":"anthropic","model":"claude-3-7-sonnet-20250219","duration_seconds":0.144,"success":true,"tokens":{},"call_count":59},"pid":110158}
{"timestamp":"2025-06-25 17:54:55","session_id":"20250625_173119","level":"INFO","message":"Model response received successfully","context":{"provider":"anthropic","model":"claude-3-7-sonnet-20250219","response_length":25,"duration_seconds":0.144},"pid":110158}
{"timestamp":"2025-06-25 17:54:55","session_id":"20250625_173119","level":"INFO","message":"Discussion prediction for cluster 5","context":{"cluster_id":"5","event_type":"prediction","data":{"model":"claude-3-7-sonnet-20250219","round":1,"prediction":"Error: No valid responses"}},"pid":110158}
{"timestamp":"2025-06-25 17:54:55","session_id":"20250625_173119","level":"INFO","message":"Initialized openai processor","context":{"provider":"openai"},"pid":110158}
{"timestamp":"2025-06-25 17:54:55","session_id":"20250625_173119","level":"INFO","message":"Starting openai API request","context":{"model":"gpt-4o","provider":"openai"},"pid":110158} {"timestamp":"2025-06-25 17:54:55","session_id":"20250625_173119","level":"ERROR","message":"OpenAI API request failed","context":{"error":"You exceeded your current quota, please check your plan and billing details. For more information on this error, read the docs: https://platform.openai.com/docs/guides/error-codes/api-errors.","provider":"openai","model":"gpt-4o","status_code":429},"pid":110158}
{"timestamp":"2025-06-25 17:54:55","session_id":"20250625_173119","level":"ERROR","message":"Failed to process chunk 1: OpenAI API request failed: You exceeded your current quota, please check your plan and billing details. For more information on this error, read the docs: https://platform.openai.com/docs/guides/error-codes/api-errors.","context":{"provider":"openai","model":"gpt-4o","chunk":1,"error":"OpenAI API request failed: You exceeded your current quota, please check your plan and billing details. For more information on this error, read the docs: https://platform.openai.com/docs/guides/error-codes/api-errors."},"pid":110158} {"timestamp":"2025-06-25 17:54:55","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"openai","chunks_processed":1},"pid":110158} {"timestamp":"2025-06-25 17:54:55","session_id":"20250625_173119","level":"ERROR","message":"No valid responses received","context":{"provider":"openai","chunks_attempted":1},"pid":110158} {"timestamp":"2025-06-25 17:54:55","session_id":"20250625_173119","level":"INFO","message":"API call completed: openai/gpt-4o (0.175s)","context":{"provider":"openai","model":"gpt-4o","duration_seconds":0.175,"success":true,"tokens":{},"call_count":60},"pid":110158}
{"timestamp":"2025-06-25 17:54:55","session_id":"20250625_173119","level":"INFO","message":"API call completed: openai/gpt-4o (0.177s)","context":{"provider":"openai","model":"gpt-4o","duration_seconds":0.177,"success":true,"tokens":{},"call_count":61},"pid":110158}
{"timestamp":"2025-06-25 17:54:55","session_id":"20250625_173119","level":"INFO","message":"Model response received successfully","context":{"provider":"openai","model":"gpt-4o","response_length":25,"duration_seconds":0.177},"pid":110158}
{"timestamp":"2025-06-25 17:54:55","session_id":"20250625_173119","level":"INFO","message":"Discussion prediction for cluster 5","context":{"cluster_id":"5","event_type":"prediction","data":{"model":"gpt-4o","round":1,"prediction":"Error: No valid responses"}},"pid":110158}
{"timestamp":"2025-06-25 17:54:55","session_id":"20250625_173119","level":"WARN","message":"Model gemini-1.5-pro failed to provide valid response for cluster 5","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:54:55","session_id":"20250625_173119","level":"WARN","message":"Model grok-3-latest failed to provide valid response for cluster 5","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:54:55","session_id":"20250625_173119","level":"WARN","message":"Model claude-3-7-sonnet-20250219 failed to provide valid response for cluster 5","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:54:55","session_id":"20250625_173119","level":"WARN","message":"Model gpt-4o failed to provide valid response for cluster 5","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:54:55","session_id":"20250625_173119","level":"WARN","message":"Only 1 valid responses received for cluster 5. Skipping discussion.","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:54:55","session_id":"20250625_173119","level":"INFO","message":"Saved result to cache for cluster 5","context":{"cluster_id":"5"},"pid":110158}
{"timestamp":"2025-06-25 17:54:55","session_id":"20250625_173119","level":"INFO","message":"Completed discussion for cluster 5","context":{"cluster_id":"5"},"pid":110158} Completed discussion for cluster 5{"timestamp":"2025-06-25 17:54:55","session_id":"20250625_173119","level":"INFO","message":"Starting discussion for cluster 6...","context":{"cluster_id":"6"},"pid":110158}
Starting discussion for cluster 6...{"timestamp":"2025-06-25 17:54:55","session_id":"20250625_173119","level":"INFO","message":"Discussion start for cluster 6","context":{"cluster_id":"6","event_type":"start","data":{"tissue_name":"human blood CD4 T cells","marker_genes":"HLA-DQA2,SYT4,CCL17,EGFL6,CA2,TNFRSF4,IGHE,TIGIT,BACE2,RXFP1"}},"pid":110158}
{"timestamp":"2025-06-25 17:54:55","session_id":"20250625_173119","level":"INFO","message":"Initialized gemini processor","context":{"provider":"gemini"},"pid":110158}
{"timestamp":"2025-06-25 17:54:55","session_id":"20250625_173119","level":"INFO","message":"Starting gemini API request","context":{"model":"gemini-2.0-flash","provider":"gemini"},"pid":110158}
{"timestamp":"2025-06-25 17:55:01","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"gemini","chunks_processed":1},"pid":110158}
{"timestamp":"2025-06-25 17:55:01","session_id":"20250625_173119","level":"INFO","message":"Results consolidated successfully","context":{"provider":"gemini","valid_chunks":1,"total_lines":15},"pid":110158}
{"timestamp":"2025-06-25 17:55:01","session_id":"20250625_173119","level":"INFO","message":"API call completed: gemini/gemini-2.0-flash (5.960s)","context":{"provider":"gemini","model":"gemini-2.0-flash","duration_seconds":5.96,"success":true,"tokens":{},"call_count":62},"pid":110158}
{"timestamp":"2025-06-25 17:55:01","session_id":"20250625_173119","level":"INFO","message":"API call completed: gemini/gemini-2.0-flash (5.962s)","context":{"provider":"gemini","model":"gemini-2.0-flash","duration_seconds":5.962,"success":true,"tokens":{},"call_count":63},"pid":110158}
{"timestamp":"2025-06-25 17:55:01","session_id":"20250625_173119","level":"INFO","message":"Model response received successfully","context":{"provider":"gemini","model":"gemini-2.0-flash","response_length":[25,0,80,0,612,0,8,234,301,217,90,0,391,0,819],"duration_seconds":5.962},"pid":110158}
{"timestamp":"2025-06-25 17:55:01","session_id":"20250625_173119","level":"INFO","message":"Discussion prediction for cluster 6","context":{"cluster_id":"6","event_type":"prediction","data":{"model":"gemini-2.0-flash","round":1,"prediction":["CELL TYPE: Th2-like cells","","GROUNDS: The cluster expresses *CCL17*, *TNFRSF4* (OX40), *IGHE* and *HLA-DQA2*.","","WARRANT: *CCL17* is a chemokine strongly associated with the recruitment of Th2 cells. *TNFRSF4* (OX40) is a costimulatory molecule that is upregulated upon T cell activation, with higher expression often observed in Th2 cells. *IGHE* codes for IgE heavy chain. While CD4 T cells do not produce IgE directly, Th2 cells are crucial for promoting B cell class switching to IgE production. *HLA-DQA2* is an MHC class II molecule involved in antigen presentation, critical for T cell activation and interaction. The presence of these genes collectively points towards a Th2-skewed phenotype in activated CD4 T cells.","","BACKING:","* **CCL17 and Th2 recruitment:** CCL17 is a key chemokine involved in the recruitment of CCR4-expressing Th2 cells to sites of inflammation in allergic diseases. (Vogel, M., et al. (2010). *J Allergy Clin Immunol*. 125(2): 436-443.)","* **OX40 (TNFRSF4) and Th2 differentiation:** OX40-OX40L interactions are crucial for the survival, expansion, and cytokine production of T cells, especially Th2 cells. OX40 signaling can promote Th2 differentiation by increasing GATA-3 expression. (Croft, M. (2010). *Annu Rev Immunol*. 28: 51-78.)","* **Th2 cells and IgE production:** Th2 cells secrete cytokines like IL-4 and IL-13, which are essential for inducing B cell class switching to IgE production. (Romagnani, S. (2000). *Eur Respir J*. 16(4): 671-680.)","* **MHC Class II (HLA-DQA2):** Necessary for antigen presentation and T cell activation.","","QUALIFIER: Probable. While these markers are suggestive of Th2-like cells, especially with the presence of *CCL17*, a more definitive classification would require additional markers, such as IL-4, IL-5, and IL-13, as well as functional assays to confirm cytokine production. The cell population may be heterogeneous, containing cells with Th2 tendencies rather than purely defined Th2 cells.","","REBUTTAL: The lack of prediction from other models like gemini-1.5-pro, grok-3-latest, claude-3-7-sonnet-20250219, and gpt-4o suggests that these models either lack the granularity or the specific knowledge base to definitively identify this cluster. The presence of *SYT4*, *EGFL6*, *CA2*, *TIGIT*, *BACE2*, and *RXFP1* may be contributing to the uncertainty for the models. These markers are less commonly associated with specific T cell subsets and may indicate a more complex or unconventional T cell type, or simply reflect a specific activation state. While these markers might indicate other functions or co-expression, the combined expression of *CCL17*, *TNFRSF4*, *IGHE* and *HLA-DQA2* strongly suggests a Th2-biased phenotype. Further investigation would be needed to fully characterize this cell population."]}},"pid":110158}
{"timestamp":"2025-06-25 17:55:01","session_id":"20250625_173119","level":"INFO","message":"Initialized gemini processor","context":{"provider":"gemini"},"pid":110158}
{"timestamp":"2025-06-25 17:55:01","session_id":"20250625_173119","level":"INFO","message":"Starting gemini API request","context":{"model":"gemini-1.5-pro","provider":"gemini"},"pid":110158} {"timestamp":"2025-06-25 17:55:01","session_id":"20250625_173119","level":"ERROR","message":"Gemini API request failed","context":{"error":"You exceeded your current quota, please check your plan and billing details. For more information on this error, head to: https://ai.google.dev/gemini-api/docs/rate-limits.","provider":"gemini","model":"gemini-1.5-pro","status_code":429},"pid":110158}
{"timestamp":"2025-06-25 17:55:01","session_id":"20250625_173119","level":"ERROR","message":"Failed to process chunk 1: Gemini API request failed: You exceeded your current quota, please check your plan and billing details. For more information on this error, head to: https://ai.google.dev/gemini-api/docs/rate-limits.","context":{"provider":"gemini","model":"gemini-1.5-pro","chunk":1,"error":"Gemini API request failed: You exceeded your current quota, please check your plan and billing details. For more information on this error, head to: https://ai.google.dev/gemini-api/docs/rate-limits."},"pid":110158} {"timestamp":"2025-06-25 17:55:01","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"gemini","chunks_processed":1},"pid":110158} {"timestamp":"2025-06-25 17:55:01","session_id":"20250625_173119","level":"ERROR","message":"No valid responses received","context":{"provider":"gemini","chunks_attempted":1},"pid":110158} {"timestamp":"2025-06-25 17:55:01","session_id":"20250625_173119","level":"INFO","message":"API call completed: gemini/gemini-1.5-pro (0.063s)","context":{"provider":"gemini","model":"gemini-1.5-pro","duration_seconds":0.063,"success":true,"tokens":{},"call_count":64},"pid":110158}
{"timestamp":"2025-06-25 17:55:01","session_id":"20250625_173119","level":"INFO","message":"API call completed: gemini/gemini-1.5-pro (0.064s)","context":{"provider":"gemini","model":"gemini-1.5-pro","duration_seconds":0.064,"success":true,"tokens":{},"call_count":65},"pid":110158}
{"timestamp":"2025-06-25 17:55:01","session_id":"20250625_173119","level":"INFO","message":"Model response received successfully","context":{"provider":"gemini","model":"gemini-1.5-pro","response_length":25,"duration_seconds":0.064},"pid":110158}
{"timestamp":"2025-06-25 17:55:01","session_id":"20250625_173119","level":"INFO","message":"Discussion prediction for cluster 6","context":{"cluster_id":"6","event_type":"prediction","data":{"model":"gemini-1.5-pro","round":1,"prediction":"Error: No valid responses"}},"pid":110158}
{"timestamp":"2025-06-25 17:55:01","session_id":"20250625_173119","level":"INFO","message":"Initialized grok processor","context":{"provider":"grok"},"pid":110158}
{"timestamp":"2025-06-25 17:55:01","session_id":"20250625_173119","level":"INFO","message":"Starting grok API request","context":{"model":"grok-3-latest","provider":"grok"},"pid":110158} {"timestamp":"2025-06-25 17:55:01","session_id":"20250625_173119","level":"ERROR","message":"Failed to process chunk 1: $ operator is invalid for atomic vectors","context":{"provider":"grok","model":"grok-3-latest","chunk":1,"error":"$ operator is invalid for atomic vectors"},"pid":110158} {"timestamp":"2025-06-25 17:55:01","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"grok","chunks_processed":1},"pid":110158} {"timestamp":"2025-06-25 17:55:01","session_id":"20250625_173119","level":"ERROR","message":"No valid responses received","context":{"provider":"grok","chunks_attempted":1},"pid":110158} {"timestamp":"2025-06-25 17:55:01","session_id":"20250625_173119","level":"INFO","message":"API call completed: grok/grok-3-latest (0.115s)","context":{"provider":"grok","model":"grok-3-latest","duration_seconds":0.115,"success":true,"tokens":{},"call_count":66},"pid":110158}
{"timestamp":"2025-06-25 17:55:01","session_id":"20250625_173119","level":"INFO","message":"API call completed: grok/grok-3-latest (0.117s)","context":{"provider":"grok","model":"grok-3-latest","duration_seconds":0.117,"success":true,"tokens":{},"call_count":67},"pid":110158}
{"timestamp":"2025-06-25 17:55:01","session_id":"20250625_173119","level":"INFO","message":"Model response received successfully","context":{"provider":"grok","model":"grok-3-latest","response_length":25,"duration_seconds":0.117},"pid":110158}
{"timestamp":"2025-06-25 17:55:01","session_id":"20250625_173119","level":"INFO","message":"Discussion prediction for cluster 6","context":{"cluster_id":"6","event_type":"prediction","data":{"model":"grok-3-latest","round":1,"prediction":"Error: No valid responses"}},"pid":110158}
{"timestamp":"2025-06-25 17:55:01","session_id":"20250625_173119","level":"INFO","message":"Initialized anthropic processor","context":{"provider":"anthropic"},"pid":110158}
{"timestamp":"2025-06-25 17:55:01","session_id":"20250625_173119","level":"INFO","message":"Starting anthropic API request","context":{"model":"claude-3-7-sonnet-20250219","provider":"anthropic"},"pid":110158} {"timestamp":"2025-06-25 17:55:01","session_id":"20250625_173119","level":"ERROR","message":"Anthropic API request failed","context":{"provider":"anthropic","model":"claude-3-7-sonnet-20250219","status_code":400,"error":"Your credit balance is too low to access the Anthropic API. Please go to Plans & Billing to upgrade or purchase credits."},"pid":110158}
{"timestamp":"2025-06-25 17:55:01","session_id":"20250625_173119","level":"ERROR","message":"Failed to process chunk 1: Anthropic API request failed: Your credit balance is too low to access the Anthropic API. Please go to Plans & Billing to upgrade or purchase credits.","context":{"provider":"anthropic","model":"claude-3-7-sonnet-20250219","chunk":1,"error":"Anthropic API request failed: Your credit balance is too low to access the Anthropic API. Please go to Plans & Billing to upgrade or purchase credits."},"pid":110158} {"timestamp":"2025-06-25 17:55:01","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"anthropic","chunks_processed":1},"pid":110158} {"timestamp":"2025-06-25 17:55:01","session_id":"20250625_173119","level":"ERROR","message":"No valid responses received","context":{"provider":"anthropic","chunks_attempted":1},"pid":110158} {"timestamp":"2025-06-25 17:55:01","session_id":"20250625_173119","level":"INFO","message":"API call completed: anthropic/claude-3-7-sonnet-20250219 (0.176s)","context":{"provider":"anthropic","model":"claude-3-7-sonnet-20250219","duration_seconds":0.176,"success":true,"tokens":{},"call_count":68},"pid":110158}
{"timestamp":"2025-06-25 17:55:01","session_id":"20250625_173119","level":"INFO","message":"API call completed: anthropic/claude-3-7-sonnet-20250219 (0.178s)","context":{"provider":"anthropic","model":"claude-3-7-sonnet-20250219","duration_seconds":0.178,"success":true,"tokens":{},"call_count":69},"pid":110158}
{"timestamp":"2025-06-25 17:55:01","session_id":"20250625_173119","level":"INFO","message":"Model response received successfully","context":{"provider":"anthropic","model":"claude-3-7-sonnet-20250219","response_length":25,"duration_seconds":0.178},"pid":110158}
{"timestamp":"2025-06-25 17:55:01","session_id":"20250625_173119","level":"INFO","message":"Discussion prediction for cluster 6","context":{"cluster_id":"6","event_type":"prediction","data":{"model":"claude-3-7-sonnet-20250219","round":1,"prediction":"Error: No valid responses"}},"pid":110158}
{"timestamp":"2025-06-25 17:55:01","session_id":"20250625_173119","level":"INFO","message":"Initialized openai processor","context":{"provider":"openai"},"pid":110158}
{"timestamp":"2025-06-25 17:55:01","session_id":"20250625_173119","level":"INFO","message":"Starting openai API request","context":{"model":"gpt-4o","provider":"openai"},"pid":110158} {"timestamp":"2025-06-25 17:55:02","session_id":"20250625_173119","level":"ERROR","message":"OpenAI API request failed","context":{"error":"You exceeded your current quota, please check your plan and billing details. For more information on this error, read the docs: https://platform.openai.com/docs/guides/error-codes/api-errors.","provider":"openai","model":"gpt-4o","status_code":429},"pid":110158}
{"timestamp":"2025-06-25 17:55:02","session_id":"20250625_173119","level":"ERROR","message":"Failed to process chunk 1: OpenAI API request failed: You exceeded your current quota, please check your plan and billing details. For more information on this error, read the docs: https://platform.openai.com/docs/guides/error-codes/api-errors.","context":{"provider":"openai","model":"gpt-4o","chunk":1,"error":"OpenAI API request failed: You exceeded your current quota, please check your plan and billing details. For more information on this error, read the docs: https://platform.openai.com/docs/guides/error-codes/api-errors."},"pid":110158} {"timestamp":"2025-06-25 17:55:02","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"openai","chunks_processed":1},"pid":110158} {"timestamp":"2025-06-25 17:55:02","session_id":"20250625_173119","level":"ERROR","message":"No valid responses received","context":{"provider":"openai","chunks_attempted":1},"pid":110158} {"timestamp":"2025-06-25 17:55:02","session_id":"20250625_173119","level":"INFO","message":"API call completed: openai/gpt-4o (0.200s)","context":{"provider":"openai","model":"gpt-4o","duration_seconds":0.2,"success":true,"tokens":{},"call_count":70},"pid":110158}
{"timestamp":"2025-06-25 17:55:02","session_id":"20250625_173119","level":"INFO","message":"API call completed: openai/gpt-4o (0.202s)","context":{"provider":"openai","model":"gpt-4o","duration_seconds":0.202,"success":true,"tokens":{},"call_count":71},"pid":110158}
{"timestamp":"2025-06-25 17:55:02","session_id":"20250625_173119","level":"INFO","message":"Model response received successfully","context":{"provider":"openai","model":"gpt-4o","response_length":25,"duration_seconds":0.202},"pid":110158}
{"timestamp":"2025-06-25 17:55:02","session_id":"20250625_173119","level":"INFO","message":"Discussion prediction for cluster 6","context":{"cluster_id":"6","event_type":"prediction","data":{"model":"gpt-4o","round":1,"prediction":"Error: No valid responses"}},"pid":110158}
{"timestamp":"2025-06-25 17:55:02","session_id":"20250625_173119","level":"WARN","message":"Model gemini-1.5-pro failed to provide valid response for cluster 6","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:55:02","session_id":"20250625_173119","level":"WARN","message":"Model grok-3-latest failed to provide valid response for cluster 6","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:55:02","session_id":"20250625_173119","level":"WARN","message":"Model claude-3-7-sonnet-20250219 failed to provide valid response for cluster 6","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:55:02","session_id":"20250625_173119","level":"WARN","message":"Model gpt-4o failed to provide valid response for cluster 6","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:55:02","session_id":"20250625_173119","level":"WARN","message":"Only 1 valid responses received for cluster 6. Skipping discussion.","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:55:02","session_id":"20250625_173119","level":"INFO","message":"Saved result to cache for cluster 6","context":{"cluster_id":"6"},"pid":110158}
{"timestamp":"2025-06-25 17:55:02","session_id":"20250625_173119","level":"INFO","message":"Completed discussion for cluster 6","context":{"cluster_id":"6"},"pid":110158} Completed discussion for cluster 6{"timestamp":"2025-06-25 17:55:02","session_id":"20250625_173119","level":"INFO","message":"Starting discussion for cluster 7...","context":{"cluster_id":"7"},"pid":110158}
Starting discussion for cluster 7...{"timestamp":"2025-06-25 17:55:02","session_id":"20250625_173119","level":"INFO","message":"Discussion start for cluster 7","context":{"cluster_id":"7","event_type":"start","data":{"tissue_name":"human blood CD4 T cells","marker_genes":"TRAV17,TOP2A,TRAV9-2,ASPM,MXD3,NUSAP1,SGO2,CCNA2,CDKN2A,KIFC1"}},"pid":110158}
{"timestamp":"2025-06-25 17:55:02","session_id":"20250625_173119","level":"INFO","message":"Initialized gemini processor","context":{"provider":"gemini"},"pid":110158}
{"timestamp":"2025-06-25 17:55:02","session_id":"20250625_173119","level":"INFO","message":"Starting gemini API request","context":{"model":"gemini-2.0-flash","provider":"gemini"},"pid":110158}
{"timestamp":"2025-06-25 17:55:08","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"gemini","chunks_processed":1},"pid":110158}
{"timestamp":"2025-06-25 17:55:08","session_id":"20250625_173119","level":"INFO","message":"Results consolidated successfully","context":{"provider":"gemini","valid_chunks":1,"total_lines":20},"pid":110158}
{"timestamp":"2025-06-25 17:55:08","session_id":"20250625_173119","level":"INFO","message":"API call completed: gemini/gemini-2.0-flash (6.678s)","context":{"provider":"gemini","model":"gemini-2.0-flash","duration_seconds":6.678,"success":true,"tokens":{},"call_count":72},"pid":110158}
{"timestamp":"2025-06-25 17:55:08","session_id":"20250625_173119","level":"INFO","message":"API call completed: gemini/gemini-2.0-flash (6.679s)","context":{"provider":"gemini","model":"gemini-2.0-flash","duration_seconds":6.679,"success":true,"tokens":{},"call_count":73},"pid":110158}
{"timestamp":"2025-06-25 17:55:08","session_id":"20250625_173119","level":"INFO","message":"Model response received successfully","context":{"provider":"gemini","model":"gemini-2.0-flash","response_length":[25,0,106,0,362,0,8,185,205,227,217,177,306,182,126,279,0,154,0,756],"duration_seconds":6.679},"pid":110158}
{"timestamp":"2025-06-25 17:55:08","session_id":"20250625_173119","level":"INFO","message":"Discussion prediction for cluster 7","context":{"cluster_id":"7","event_type":"prediction","data":{"model":"gemini-2.0-flash","round":1,"prediction":["CELL TYPE: Cycling T cell","","GROUNDS: The cluster expresses TRAV17, TOP2A, TRAV9-2, ASPM, MXD3, NUSAP1, SGO2, CCNA2, CDKN2A, and KIFC1.","","WARRANT: The presence of genes like TOP2A, ASPM, NUSAP1, SGO2, CCNA2, CDKN2A, and KIFC1 strongly indicates active cell cycling/proliferation. These genes are known to be upregulated during specific phases of the cell cycle and are crucial for cell division. While TRAV17 and TRAV9-2 suggest T cell origin, the cell cycle genes suggest they are actively dividing.","","BACKING:","* **TOP2A:** Topoisomerase II Alpha is essential for DNA replication and chromosome segregation during cell division (Wang, 2002). It's a commonly used marker for proliferating cells.","* **ASPM:** Abnormal Spindle Microtubule Assembly is crucial for mitotic spindle formation and chromosome segregation. Overexpression is associated with cell proliferation and cancer (Fish et al., 2006).","* **NUSAP1:** Nucleolar and Spindle Associated Protein 1 plays a critical role in mitotic spindle organization and chromosome stability. Elevated NUSAP1 expression is associated with cell proliferation (Ribbeck et al., 2006).","* **SGO2 (SGOL2):** Shugoshin 2 is involved in chromosome cohesion during mitosis and meiosis, protecting centromeric cohesion during prophase. It's essential for accurate chromosome segregation (Tang et al., 2004).","* **CCNA2:** Cyclin A2 is a key regulator of the cell cycle, specifically during S and G2 phases. It's involved in DNA replication and entry into mitosis (Diril et al., 2012).","* **CDKN2A (p16):** While often considered a tumor suppressor, CDKN2A expression can increase in cycling cells during the G1 phase, especially under stress or during controlled proliferation (Sharpless & DePinho, 1999). However, its role can be complex and sometimes paradoxical depending on the context.","* **KIFC1:** Kinesin Family Member C1 is a mitotic kinesin involved in spindle pole organization and chromosome segregation. It's required for proper cell division (Walczak, 2003).","* **TRAV17 and TRAV9-2:** These are T cell receptor alpha variable (TRAV) genes. Their presence confirms the T cell lineage.","* **MXD3:** Max Dimerization Protein 3 is a transcriptional repressor that can influence cell cycle progression and differentiation. Its specific role in cycling T cells isn't as directly linked as the other cell cycle genes, but it can be involved in regulating proliferation.","","QUALIFIER: Almost certainly. The strong presence of multiple genes directly involved in cell cycling makes the \"cycling T cell\" designation highly likely.","","REBUTTAL: While the gemini-2.0-flash model only predicted \"T cells,\" our conclusion of \"cycling T cell\" is more precise, accounting for the cell cycle marker gene expression. The other models predicted \"No prediction,\" likely because the model's training data or internal logic does not prioritize linking these genes to cycling cells, or it may lack the granularity to make such a specific classification. It's possible that a small subset of the cells within the cluster are not actively cycling, but the overall gene expression profile strongly suggests the dominant population is undergoing cell division. The role of CDKN2A can be context-dependent, and its expression does not negate the strong indication of active cycling provided by other markers."]}},"pid":110158}
{"timestamp":"2025-06-25 17:55:08","session_id":"20250625_173119","level":"INFO","message":"Initialized gemini processor","context":{"provider":"gemini"},"pid":110158}
{"timestamp":"2025-06-25 17:55:08","session_id":"20250625_173119","level":"INFO","message":"Starting gemini API request","context":{"model":"gemini-1.5-pro","provider":"gemini"},"pid":110158} {"timestamp":"2025-06-25 17:55:08","session_id":"20250625_173119","level":"ERROR","message":"Gemini API request failed","context":{"error":"You exceeded your current quota, please check your plan and billing details. For more information on this error, head to: https://ai.google.dev/gemini-api/docs/rate-limits.","provider":"gemini","model":"gemini-1.5-pro","status_code":429},"pid":110158}
{"timestamp":"2025-06-25 17:55:08","session_id":"20250625_173119","level":"ERROR","message":"Failed to process chunk 1: Gemini API request failed: You exceeded your current quota, please check your plan and billing details. For more information on this error, head to: https://ai.google.dev/gemini-api/docs/rate-limits.","context":{"provider":"gemini","model":"gemini-1.5-pro","chunk":1,"error":"Gemini API request failed: You exceeded your current quota, please check your plan and billing details. For more information on this error, head to: https://ai.google.dev/gemini-api/docs/rate-limits."},"pid":110158} {"timestamp":"2025-06-25 17:55:08","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"gemini","chunks_processed":1},"pid":110158} {"timestamp":"2025-06-25 17:55:08","session_id":"20250625_173119","level":"ERROR","message":"No valid responses received","context":{"provider":"gemini","chunks_attempted":1},"pid":110158} {"timestamp":"2025-06-25 17:55:08","session_id":"20250625_173119","level":"INFO","message":"API call completed: gemini/gemini-1.5-pro (0.062s)","context":{"provider":"gemini","model":"gemini-1.5-pro","duration_seconds":0.062,"success":true,"tokens":{},"call_count":74},"pid":110158}
{"timestamp":"2025-06-25 17:55:08","session_id":"20250625_173119","level":"INFO","message":"API call completed: gemini/gemini-1.5-pro (0.064s)","context":{"provider":"gemini","model":"gemini-1.5-pro","duration_seconds":0.064,"success":true,"tokens":{},"call_count":75},"pid":110158}
{"timestamp":"2025-06-25 17:55:08","session_id":"20250625_173119","level":"INFO","message":"Model response received successfully","context":{"provider":"gemini","model":"gemini-1.5-pro","response_length":25,"duration_seconds":0.064},"pid":110158}
{"timestamp":"2025-06-25 17:55:08","session_id":"20250625_173119","level":"INFO","message":"Discussion prediction for cluster 7","context":{"cluster_id":"7","event_type":"prediction","data":{"model":"gemini-1.5-pro","round":1,"prediction":"Error: No valid responses"}},"pid":110158}
{"timestamp":"2025-06-25 17:55:08","session_id":"20250625_173119","level":"INFO","message":"Initialized grok processor","context":{"provider":"grok"},"pid":110158}
{"timestamp":"2025-06-25 17:55:08","session_id":"20250625_173119","level":"INFO","message":"Starting grok API request","context":{"model":"grok-3-latest","provider":"grok"},"pid":110158} {"timestamp":"2025-06-25 17:55:09","session_id":"20250625_173119","level":"ERROR","message":"Failed to process chunk 1: $ operator is invalid for atomic vectors","context":{"provider":"grok","model":"grok-3-latest","chunk":1,"error":"$ operator is invalid for atomic vectors"},"pid":110158} {"timestamp":"2025-06-25 17:55:09","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"grok","chunks_processed":1},"pid":110158} {"timestamp":"2025-06-25 17:55:09","session_id":"20250625_173119","level":"ERROR","message":"No valid responses received","context":{"provider":"grok","chunks_attempted":1},"pid":110158} {"timestamp":"2025-06-25 17:55:09","session_id":"20250625_173119","level":"INFO","message":"API call completed: grok/grok-3-latest (0.114s)","context":{"provider":"grok","model":"grok-3-latest","duration_seconds":0.114,"success":true,"tokens":{},"call_count":76},"pid":110158}
{"timestamp":"2025-06-25 17:55:09","session_id":"20250625_173119","level":"INFO","message":"API call completed: grok/grok-3-latest (0.116s)","context":{"provider":"grok","model":"grok-3-latest","duration_seconds":0.116,"success":true,"tokens":{},"call_count":77},"pid":110158}
{"timestamp":"2025-06-25 17:55:09","session_id":"20250625_173119","level":"INFO","message":"Model response received successfully","context":{"provider":"grok","model":"grok-3-latest","response_length":25,"duration_seconds":0.116},"pid":110158}
{"timestamp":"2025-06-25 17:55:09","session_id":"20250625_173119","level":"INFO","message":"Discussion prediction for cluster 7","context":{"cluster_id":"7","event_type":"prediction","data":{"model":"grok-3-latest","round":1,"prediction":"Error: No valid responses"}},"pid":110158}
{"timestamp":"2025-06-25 17:55:09","session_id":"20250625_173119","level":"INFO","message":"Initialized anthropic processor","context":{"provider":"anthropic"},"pid":110158}
{"timestamp":"2025-06-25 17:55:09","session_id":"20250625_173119","level":"INFO","message":"Starting anthropic API request","context":{"model":"claude-3-7-sonnet-20250219","provider":"anthropic"},"pid":110158} {"timestamp":"2025-06-25 17:55:09","session_id":"20250625_173119","level":"ERROR","message":"Anthropic API request failed","context":{"provider":"anthropic","model":"claude-3-7-sonnet-20250219","status_code":400,"error":"Your credit balance is too low to access the Anthropic API. Please go to Plans & Billing to upgrade or purchase credits."},"pid":110158}
{"timestamp":"2025-06-25 17:55:09","session_id":"20250625_173119","level":"ERROR","message":"Failed to process chunk 1: Anthropic API request failed: Your credit balance is too low to access the Anthropic API. Please go to Plans & Billing to upgrade or purchase credits.","context":{"provider":"anthropic","model":"claude-3-7-sonnet-20250219","chunk":1,"error":"Anthropic API request failed: Your credit balance is too low to access the Anthropic API. Please go to Plans & Billing to upgrade or purchase credits."},"pid":110158} {"timestamp":"2025-06-25 17:55:09","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"anthropic","chunks_processed":1},"pid":110158} {"timestamp":"2025-06-25 17:55:09","session_id":"20250625_173119","level":"ERROR","message":"No valid responses received","context":{"provider":"anthropic","chunks_attempted":1},"pid":110158} {"timestamp":"2025-06-25 17:55:09","session_id":"20250625_173119","level":"INFO","message":"API call completed: anthropic/claude-3-7-sonnet-20250219 (0.204s)","context":{"provider":"anthropic","model":"claude-3-7-sonnet-20250219","duration_seconds":0.204,"success":true,"tokens":{},"call_count":78},"pid":110158}
{"timestamp":"2025-06-25 17:55:09","session_id":"20250625_173119","level":"INFO","message":"API call completed: anthropic/claude-3-7-sonnet-20250219 (0.205s)","context":{"provider":"anthropic","model":"claude-3-7-sonnet-20250219","duration_seconds":0.205,"success":true,"tokens":{},"call_count":79},"pid":110158}
{"timestamp":"2025-06-25 17:55:09","session_id":"20250625_173119","level":"INFO","message":"Model response received successfully","context":{"provider":"anthropic","model":"claude-3-7-sonnet-20250219","response_length":25,"duration_seconds":0.205},"pid":110158}
{"timestamp":"2025-06-25 17:55:09","session_id":"20250625_173119","level":"INFO","message":"Discussion prediction for cluster 7","context":{"cluster_id":"7","event_type":"prediction","data":{"model":"claude-3-7-sonnet-20250219","round":1,"prediction":"Error: No valid responses"}},"pid":110158}
{"timestamp":"2025-06-25 17:55:09","session_id":"20250625_173119","level":"INFO","message":"Initialized openai processor","context":{"provider":"openai"},"pid":110158}
{"timestamp":"2025-06-25 17:55:09","session_id":"20250625_173119","level":"INFO","message":"Starting openai API request","context":{"model":"gpt-4o","provider":"openai"},"pid":110158} {"timestamp":"2025-06-25 17:55:09","session_id":"20250625_173119","level":"ERROR","message":"OpenAI API request failed","context":{"error":"You exceeded your current quota, please check your plan and billing details. For more information on this error, read the docs: https://platform.openai.com/docs/guides/error-codes/api-errors.","provider":"openai","model":"gpt-4o","status_code":429},"pid":110158}
{"timestamp":"2025-06-25 17:55:09","session_id":"20250625_173119","level":"ERROR","message":"Failed to process chunk 1: OpenAI API request failed: You exceeded your current quota, please check your plan and billing details. For more information on this error, read the docs: https://platform.openai.com/docs/guides/error-codes/api-errors.","context":{"provider":"openai","model":"gpt-4o","chunk":1,"error":"OpenAI API request failed: You exceeded your current quota, please check your plan and billing details. For more information on this error, read the docs: https://platform.openai.com/docs/guides/error-codes/api-errors."},"pid":110158} {"timestamp":"2025-06-25 17:55:09","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"openai","chunks_processed":1},"pid":110158} {"timestamp":"2025-06-25 17:55:09","session_id":"20250625_173119","level":"ERROR","message":"No valid responses received","context":{"provider":"openai","chunks_attempted":1},"pid":110158} {"timestamp":"2025-06-25 17:55:09","session_id":"20250625_173119","level":"INFO","message":"API call completed: openai/gpt-4o (0.206s)","context":{"provider":"openai","model":"gpt-4o","duration_seconds":0.206,"success":true,"tokens":{},"call_count":80},"pid":110158}
{"timestamp":"2025-06-25 17:55:09","session_id":"20250625_173119","level":"INFO","message":"API call completed: openai/gpt-4o (0.208s)","context":{"provider":"openai","model":"gpt-4o","duration_seconds":0.208,"success":true,"tokens":{},"call_count":81},"pid":110158}
{"timestamp":"2025-06-25 17:55:09","session_id":"20250625_173119","level":"INFO","message":"Model response received successfully","context":{"provider":"openai","model":"gpt-4o","response_length":25,"duration_seconds":0.208},"pid":110158}
{"timestamp":"2025-06-25 17:55:09","session_id":"20250625_173119","level":"INFO","message":"Discussion prediction for cluster 7","context":{"cluster_id":"7","event_type":"prediction","data":{"model":"gpt-4o","round":1,"prediction":"Error: No valid responses"}},"pid":110158}
{"timestamp":"2025-06-25 17:55:09","session_id":"20250625_173119","level":"WARN","message":"Model gemini-1.5-pro failed to provide valid response for cluster 7","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:55:09","session_id":"20250625_173119","level":"WARN","message":"Model grok-3-latest failed to provide valid response for cluster 7","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:55:09","session_id":"20250625_173119","level":"WARN","message":"Model claude-3-7-sonnet-20250219 failed to provide valid response for cluster 7","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:55:09","session_id":"20250625_173119","level":"WARN","message":"Model gpt-4o failed to provide valid response for cluster 7","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:55:09","session_id":"20250625_173119","level":"WARN","message":"Only 1 valid responses received for cluster 7. Skipping discussion.","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:55:09","session_id":"20250625_173119","level":"INFO","message":"Saved result to cache for cluster 7","context":{"cluster_id":"7"},"pid":110158}
{"timestamp":"2025-06-25 17:55:09","session_id":"20250625_173119","level":"INFO","message":"Completed discussion for cluster 7","context":{"cluster_id":"7"},"pid":110158} Completed discussion for cluster 7{"timestamp":"2025-06-25 17:55:09","session_id":"20250625_173119","level":"INFO","message":"Starting discussion for cluster 8...","context":{"cluster_id":"8"},"pid":110158}
Starting discussion for cluster 8...{"timestamp":"2025-06-25 17:55:09","session_id":"20250625_173119","level":"INFO","message":"Discussion start for cluster 8","context":{"cluster_id":"8","event_type":"start","data":{"tissue_name":"human blood CD4 T cells","marker_genes":"EEF1A2,TRAV4,EGFL6,PXYLP1,TNFRSF4,TIGIT,PHLDA2,WFDC1,HLA-DQA2,GPAT3"}},"pid":110158}
{"timestamp":"2025-06-25 17:55:09","session_id":"20250625_173119","level":"INFO","message":"Initialized gemini processor","context":{"provider":"gemini"},"pid":110158}
{"timestamp":"2025-06-25 17:55:09","session_id":"20250625_173119","level":"INFO","message":"Starting gemini API request","context":{"model":"gemini-2.0-flash","provider":"gemini"},"pid":110158}
{"timestamp":"2025-06-25 17:55:15","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"gemini","chunks_processed":1},"pid":110158}
{"timestamp":"2025-06-25 17:55:15","session_id":"20250625_173119","level":"INFO","message":"Results consolidated successfully","context":{"provider":"gemini","valid_chunks":1,"total_lines":16},"pid":110158}
{"timestamp":"2025-06-25 17:55:15","session_id":"20250625_173119","level":"INFO","message":"API call completed: gemini/gemini-2.0-flash (6.122s)","context":{"provider":"gemini","model":"gemini-2.0-flash","duration_seconds":6.122,"success":true,"tokens":{},"call_count":82},"pid":110158}
{"timestamp":"2025-06-25 17:55:15","session_id":"20250625_173119","level":"INFO","message":"API call completed: gemini/gemini-2.0-flash (6.123s)","context":{"provider":"gemini","model":"gemini-2.0-flash","duration_seconds":6.123,"success":true,"tokens":{},"call_count":83},"pid":110158}
{"timestamp":"2025-06-25 17:55:15","session_id":"20250625_173119","level":"INFO","message":"Model response received successfully","context":{"provider":"gemini","model":"gemini-2.0-flash","response_length":[49,0,147,0,780,0,8,0,262,481,261,295,0,385,0,742],"duration_seconds":6.123},"pid":110158}
{"timestamp":"2025-06-25 17:55:15","session_id":"20250625_173119","level":"INFO","message":"Discussion prediction for cluster 8","context":{"cluster_id":"8","event_type":"prediction","data":{"model":"gemini-2.0-flash","round":1,"prediction":["CELL TYPE: Activated/Regulatory CD4 T cell (Treg)","","GROUNDS: The cluster expresses the following marker genes: EEF1A2, TRAV4, EGFL6, PXYLP1, TNFRSF4 (OX40), TIGIT, PHLDA2, WFDC1, HLA-DQA2, and GPAT3.","","WARRANT: The presence of several key marker genes, particularly TNFRSF4 (OX40), TIGIT, PHLDA2, and HLA-DQA2, strongly suggests an activated and potentially regulatory CD4 T cell phenotype. OX40 (TNFRSF4) is a co-stimulatory molecule expressed on activated T cells, including Tregs. TIGIT is an inhibitory receptor expressed on Tregs and other T cells, often associated with immune suppression. PHLDA2 is enriched in Tregs and involved in their suppressive function. HLA-DQA2, an MHC Class II molecule, is also found on activated T cells and can be involved in antigen presentation, a function Tregs sometimes utilize. While EEF1A2, TRAV4, EGFL6, PXYLP1, WFDC1, and GPAT3 are less specific individually, their co-expression with the key markers further supports the identification.","","BACKING:","","* **OX40 (TNFRSF4):** \"OX40 is a costimulatory molecule expressed on activated T cells, including Tregs, and promotes their survival and function\" (e.g., Croft, M. (2010). TNF superfamily members as targets for autoimmune diseases. *Cell*, *140*(2), 141-155.).","* **TIGIT:** \"TIGIT is an inhibitory receptor expressed on T cells, including Tregs, and plays a role in immune suppression.\" (e.g., Lozano, E., & Sancho, D. (2020). The TIGIT/CD155 axis in anti-tumour immunity. *Immunology*, *160*(1), 1-13.). Studies show TIGIT+ Tregs have enhanced suppressive capacity (e.g., Joller, N., et al. (2011). Treg cells with suppressive function selectively express latency-associated peptide to modulate APC function. *Immunity*, *35*(4), 621-631.)","* **PHLDA2:** \"PHLDA2 is a marker of regulatory T cells and contributes to their suppressive function.\" (e.g., Rauch, U., et al. (2013). PHLDA2 expression defines suppressive human regulatory T cells. *Journal of Experimental Medicine*, *210*(8), 1579-1594.).","* **HLA-DQA2:** Expression of MHC-II molecules on Tregs can be important for their function. They can present antigens to interact with other immune cells. (e.g., Vignali, D. A. A., Collison, L. W., Workman, C. J. (2008). How regulatory T cells work. Nature Reviews Immunology, 8(7), 523-532.)","","QUALIFIER: Probable. While the presence of these markers strongly indicates an activated/regulatory CD4 T cell (Treg) phenotype, further characterization (e.g., FOXP3 staining, functional assays) would be necessary for definite confirmation. It is difficult to completely exclude the possibility of a highly activated effector T cell population expressing some Treg-associated markers.","","REBUTTAL: The other models provided no prediction. This may indicate a difficult-to-classify cell state or a lack of specific training data encompassing this precise combination of markers in their respective models. Some of the genes (e.g., EEF1A2) are broadly expressed, so their presence alone wouldn't be decisive. However, the combination of OX40, TIGIT, PHLDA2, and HLA-DQA2 is highly suggestive of an activated/regulatory phenotype, mitigating the ambiguity introduced by the more broadly expressed genes. The exact subtype of Treg (e.g., effector Treg, tissue-resident Treg) would require additional markers and functional data to determine. Also, the expression levels of these genes would be helpful to know, which are not provided."]}},"pid":110158}
{"timestamp":"2025-06-25 17:55:15","session_id":"20250625_173119","level":"INFO","message":"Initialized gemini processor","context":{"provider":"gemini"},"pid":110158}
{"timestamp":"2025-06-25 17:55:15","session_id":"20250625_173119","level":"INFO","message":"Starting gemini API request","context":{"model":"gemini-1.5-pro","provider":"gemini"},"pid":110158} {"timestamp":"2025-06-25 17:55:15","session_id":"20250625_173119","level":"ERROR","message":"Gemini API request failed","context":{"error":"You exceeded your current quota, please check your plan and billing details. For more information on this error, head to: https://ai.google.dev/gemini-api/docs/rate-limits.","provider":"gemini","model":"gemini-1.5-pro","status_code":429},"pid":110158}
{"timestamp":"2025-06-25 17:55:15","session_id":"20250625_173119","level":"ERROR","message":"Failed to process chunk 1: Gemini API request failed: You exceeded your current quota, please check your plan and billing details. For more information on this error, head to: https://ai.google.dev/gemini-api/docs/rate-limits.","context":{"provider":"gemini","model":"gemini-1.5-pro","chunk":1,"error":"Gemini API request failed: You exceeded your current quota, please check your plan and billing details. For more information on this error, head to: https://ai.google.dev/gemini-api/docs/rate-limits."},"pid":110158} {"timestamp":"2025-06-25 17:55:15","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"gemini","chunks_processed":1},"pid":110158} {"timestamp":"2025-06-25 17:55:15","session_id":"20250625_173119","level":"ERROR","message":"No valid responses received","context":{"provider":"gemini","chunks_attempted":1},"pid":110158} {"timestamp":"2025-06-25 17:55:15","session_id":"20250625_173119","level":"INFO","message":"API call completed: gemini/gemini-1.5-pro (0.068s)","context":{"provider":"gemini","model":"gemini-1.5-pro","duration_seconds":0.068,"success":true,"tokens":{},"call_count":84},"pid":110158}
{"timestamp":"2025-06-25 17:55:15","session_id":"20250625_173119","level":"INFO","message":"API call completed: gemini/gemini-1.5-pro (0.069s)","context":{"provider":"gemini","model":"gemini-1.5-pro","duration_seconds":0.069,"success":true,"tokens":{},"call_count":85},"pid":110158}
{"timestamp":"2025-06-25 17:55:15","session_id":"20250625_173119","level":"INFO","message":"Model response received successfully","context":{"provider":"gemini","model":"gemini-1.5-pro","response_length":25,"duration_seconds":0.069},"pid":110158}
{"timestamp":"2025-06-25 17:55:15","session_id":"20250625_173119","level":"INFO","message":"Discussion prediction for cluster 8","context":{"cluster_id":"8","event_type":"prediction","data":{"model":"gemini-1.5-pro","round":1,"prediction":"Error: No valid responses"}},"pid":110158}
{"timestamp":"2025-06-25 17:55:15","session_id":"20250625_173119","level":"INFO","message":"Initialized grok processor","context":{"provider":"grok"},"pid":110158}
{"timestamp":"2025-06-25 17:55:15","session_id":"20250625_173119","level":"INFO","message":"Starting grok API request","context":{"model":"grok-3-latest","provider":"grok"},"pid":110158} {"timestamp":"2025-06-25 17:55:15","session_id":"20250625_173119","level":"ERROR","message":"Failed to process chunk 1: $ operator is invalid for atomic vectors","context":{"provider":"grok","model":"grok-3-latest","chunk":1,"error":"$ operator is invalid for atomic vectors"},"pid":110158} {"timestamp":"2025-06-25 17:55:15","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"grok","chunks_processed":1},"pid":110158} {"timestamp":"2025-06-25 17:55:15","session_id":"20250625_173119","level":"ERROR","message":"No valid responses received","context":{"provider":"grok","chunks_attempted":1},"pid":110158} {"timestamp":"2025-06-25 17:55:15","session_id":"20250625_173119","level":"INFO","message":"API call completed: grok/grok-3-latest (0.110s)","context":{"provider":"grok","model":"grok-3-latest","duration_seconds":0.11,"success":true,"tokens":{},"call_count":86},"pid":110158}
{"timestamp":"2025-06-25 17:55:15","session_id":"20250625_173119","level":"INFO","message":"API call completed: grok/grok-3-latest (0.112s)","context":{"provider":"grok","model":"grok-3-latest","duration_seconds":0.112,"success":true,"tokens":{},"call_count":87},"pid":110158}
{"timestamp":"2025-06-25 17:55:15","session_id":"20250625_173119","level":"INFO","message":"Model response received successfully","context":{"provider":"grok","model":"grok-3-latest","response_length":25,"duration_seconds":0.112},"pid":110158}
{"timestamp":"2025-06-25 17:55:15","session_id":"20250625_173119","level":"INFO","message":"Discussion prediction for cluster 8","context":{"cluster_id":"8","event_type":"prediction","data":{"model":"grok-3-latest","round":1,"prediction":"Error: No valid responses"}},"pid":110158}
{"timestamp":"2025-06-25 17:55:15","session_id":"20250625_173119","level":"INFO","message":"Initialized anthropic processor","context":{"provider":"anthropic"},"pid":110158}
{"timestamp":"2025-06-25 17:55:15","session_id":"20250625_173119","level":"INFO","message":"Starting anthropic API request","context":{"model":"claude-3-7-sonnet-20250219","provider":"anthropic"},"pid":110158} {"timestamp":"2025-06-25 17:55:15","session_id":"20250625_173119","level":"ERROR","message":"Anthropic API request failed","context":{"provider":"anthropic","model":"claude-3-7-sonnet-20250219","status_code":400,"error":"Your credit balance is too low to access the Anthropic API. Please go to Plans & Billing to upgrade or purchase credits."},"pid":110158}
{"timestamp":"2025-06-25 17:55:15","session_id":"20250625_173119","level":"ERROR","message":"Failed to process chunk 1: Anthropic API request failed: Your credit balance is too low to access the Anthropic API. Please go to Plans & Billing to upgrade or purchase credits.","context":{"provider":"anthropic","model":"claude-3-7-sonnet-20250219","chunk":1,"error":"Anthropic API request failed: Your credit balance is too low to access the Anthropic API. Please go to Plans & Billing to upgrade or purchase credits."},"pid":110158} {"timestamp":"2025-06-25 17:55:15","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"anthropic","chunks_processed":1},"pid":110158} {"timestamp":"2025-06-25 17:55:15","session_id":"20250625_173119","level":"ERROR","message":"No valid responses received","context":{"provider":"anthropic","chunks_attempted":1},"pid":110158} {"timestamp":"2025-06-25 17:55:15","session_id":"20250625_173119","level":"INFO","message":"API call completed: anthropic/claude-3-7-sonnet-20250219 (0.156s)","context":{"provider":"anthropic","model":"claude-3-7-sonnet-20250219","duration_seconds":0.156,"success":true,"tokens":{},"call_count":88},"pid":110158}
{"timestamp":"2025-06-25 17:55:15","session_id":"20250625_173119","level":"INFO","message":"API call completed: anthropic/claude-3-7-sonnet-20250219 (0.157s)","context":{"provider":"anthropic","model":"claude-3-7-sonnet-20250219","duration_seconds":0.157,"success":true,"tokens":{},"call_count":89},"pid":110158}
{"timestamp":"2025-06-25 17:55:15","session_id":"20250625_173119","level":"INFO","message":"Model response received successfully","context":{"provider":"anthropic","model":"claude-3-7-sonnet-20250219","response_length":25,"duration_seconds":0.157},"pid":110158}
{"timestamp":"2025-06-25 17:55:15","session_id":"20250625_173119","level":"INFO","message":"Discussion prediction for cluster 8","context":{"cluster_id":"8","event_type":"prediction","data":{"model":"claude-3-7-sonnet-20250219","round":1,"prediction":"Error: No valid responses"}},"pid":110158}
{"timestamp":"2025-06-25 17:55:15","session_id":"20250625_173119","level":"INFO","message":"Initialized openai processor","context":{"provider":"openai"},"pid":110158}
{"timestamp":"2025-06-25 17:55:15","session_id":"20250625_173119","level":"INFO","message":"Starting openai API request","context":{"model":"gpt-4o","provider":"openai"},"pid":110158} {"timestamp":"2025-06-25 17:55:16","session_id":"20250625_173119","level":"ERROR","message":"OpenAI API request failed","context":{"error":"You exceeded your current quota, please check your plan and billing details. For more information on this error, read the docs: https://platform.openai.com/docs/guides/error-codes/api-errors.","provider":"openai","model":"gpt-4o","status_code":429},"pid":110158}
{"timestamp":"2025-06-25 17:55:16","session_id":"20250625_173119","level":"ERROR","message":"Failed to process chunk 1: OpenAI API request failed: You exceeded your current quota, please check your plan and billing details. For more information on this error, read the docs: https://platform.openai.com/docs/guides/error-codes/api-errors.","context":{"provider":"openai","model":"gpt-4o","chunk":1,"error":"OpenAI API request failed: You exceeded your current quota, please check your plan and billing details. For more information on this error, read the docs: https://platform.openai.com/docs/guides/error-codes/api-errors."},"pid":110158} {"timestamp":"2025-06-25 17:55:16","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"openai","chunks_processed":1},"pid":110158} {"timestamp":"2025-06-25 17:55:16","session_id":"20250625_173119","level":"ERROR","message":"No valid responses received","context":{"provider":"openai","chunks_attempted":1},"pid":110158} {"timestamp":"2025-06-25 17:55:16","session_id":"20250625_173119","level":"INFO","message":"API call completed: openai/gpt-4o (0.176s)","context":{"provider":"openai","model":"gpt-4o","duration_seconds":0.176,"success":true,"tokens":{},"call_count":90},"pid":110158}
{"timestamp":"2025-06-25 17:55:16","session_id":"20250625_173119","level":"INFO","message":"API call completed: openai/gpt-4o (0.177s)","context":{"provider":"openai","model":"gpt-4o","duration_seconds":0.177,"success":true,"tokens":{},"call_count":91},"pid":110158}
{"timestamp":"2025-06-25 17:55:16","session_id":"20250625_173119","level":"INFO","message":"Model response received successfully","context":{"provider":"openai","model":"gpt-4o","response_length":25,"duration_seconds":0.177},"pid":110158}
{"timestamp":"2025-06-25 17:55:16","session_id":"20250625_173119","level":"INFO","message":"Discussion prediction for cluster 8","context":{"cluster_id":"8","event_type":"prediction","data":{"model":"gpt-4o","round":1,"prediction":"Error: No valid responses"}},"pid":110158}
{"timestamp":"2025-06-25 17:55:16","session_id":"20250625_173119","level":"WARN","message":"Model gemini-1.5-pro failed to provide valid response for cluster 8","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:55:16","session_id":"20250625_173119","level":"WARN","message":"Model grok-3-latest failed to provide valid response for cluster 8","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:55:16","session_id":"20250625_173119","level":"WARN","message":"Model claude-3-7-sonnet-20250219 failed to provide valid response for cluster 8","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:55:16","session_id":"20250625_173119","level":"WARN","message":"Model gpt-4o failed to provide valid response for cluster 8","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:55:16","session_id":"20250625_173119","level":"WARN","message":"Only 1 valid responses received for cluster 8. Skipping discussion.","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:55:16","session_id":"20250625_173119","level":"INFO","message":"Saved result to cache for cluster 8","context":{"cluster_id":"8"},"pid":110158}
{"timestamp":"2025-06-25 17:55:16","session_id":"20250625_173119","level":"INFO","message":"Completed discussion for cluster 8","context":{"cluster_id":"8"},"pid":110158} Completed discussion for cluster 8{"timestamp":"2025-06-25 17:55:16","session_id":"20250625_173119","level":"INFO","message":"Starting discussion for cluster 9...","context":{"cluster_id":"9"},"pid":110158}
Starting discussion for cluster 9...{"timestamp":"2025-06-25 17:55:16","session_id":"20250625_173119","level":"INFO","message":"Discussion start for cluster 9","context":{"cluster_id":"9","event_type":"start","data":{"tissue_name":"human blood CD4 T cells","marker_genes":"TRAV38-2DV8,KRT1,RAB25,CST7,TTC29,LINC02752,TBX4,TNS4,WFDC1,CD5"}},"pid":110158}
{"timestamp":"2025-06-25 17:55:16","session_id":"20250625_173119","level":"INFO","message":"Initialized gemini processor","context":{"provider":"gemini"},"pid":110158}
{"timestamp":"2025-06-25 17:55:16","session_id":"20250625_173119","level":"INFO","message":"Starting gemini API request","context":{"model":"gemini-2.0-flash","provider":"gemini"},"pid":110158} {"timestamp":"2025-06-25 17:55:17","session_id":"20250625_173119","level":"ERROR","message":"Gemini API request failed","context":{"error":"The model is overloaded. Please try again later.","provider":"gemini","model":"gemini-2.0-flash","status_code":503},"pid":110158}
{"timestamp":"2025-06-25 17:55:17","session_id":"20250625_173119","level":"ERROR","message":"Failed to process chunk 1: Gemini API request failed: The model is overloaded. Please try again later.","context":{"provider":"gemini","model":"gemini-2.0-flash","chunk":1,"error":"Gemini API request failed: The model is overloaded. Please try again later."},"pid":110158} {"timestamp":"2025-06-25 17:55:17","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"gemini","chunks_processed":1},"pid":110158} {"timestamp":"2025-06-25 17:55:17","session_id":"20250625_173119","level":"ERROR","message":"No valid responses received","context":{"provider":"gemini","chunks_attempted":1},"pid":110158} {"timestamp":"2025-06-25 17:55:17","session_id":"20250625_173119","level":"INFO","message":"API call completed: gemini/gemini-2.0-flash (0.920s)","context":{"provider":"gemini","model":"gemini-2.0-flash","duration_seconds":0.92,"success":true,"tokens":{},"call_count":92},"pid":110158}
{"timestamp":"2025-06-25 17:55:17","session_id":"20250625_173119","level":"INFO","message":"API call completed: gemini/gemini-2.0-flash (0.921s)","context":{"provider":"gemini","model":"gemini-2.0-flash","duration_seconds":0.921,"success":true,"tokens":{},"call_count":93},"pid":110158}
{"timestamp":"2025-06-25 17:55:17","session_id":"20250625_173119","level":"INFO","message":"Model response received successfully","context":{"provider":"gemini","model":"gemini-2.0-flash","response_length":25,"duration_seconds":0.921},"pid":110158}
{"timestamp":"2025-06-25 17:55:17","session_id":"20250625_173119","level":"INFO","message":"Discussion prediction for cluster 9","context":{"cluster_id":"9","event_type":"prediction","data":{"model":"gemini-2.0-flash","round":1,"prediction":"Error: No valid responses"}},"pid":110158}
{"timestamp":"2025-06-25 17:55:17","session_id":"20250625_173119","level":"INFO","message":"Initialized gemini processor","context":{"provider":"gemini"},"pid":110158}
{"timestamp":"2025-06-25 17:55:17","session_id":"20250625_173119","level":"INFO","message":"Starting gemini API request","context":{"model":"gemini-1.5-pro","provider":"gemini"},"pid":110158} {"timestamp":"2025-06-25 17:55:17","session_id":"20250625_173119","level":"ERROR","message":"Gemini API request failed","context":{"error":"You exceeded your current quota, please check your plan and billing details. For more information on this error, head to: https://ai.google.dev/gemini-api/docs/rate-limits.","provider":"gemini","model":"gemini-1.5-pro","status_code":429},"pid":110158}
{"timestamp":"2025-06-25 17:55:17","session_id":"20250625_173119","level":"ERROR","message":"Failed to process chunk 1: Gemini API request failed: You exceeded your current quota, please check your plan and billing details. For more information on this error, head to: https://ai.google.dev/gemini-api/docs/rate-limits.","context":{"provider":"gemini","model":"gemini-1.5-pro","chunk":1,"error":"Gemini API request failed: You exceeded your current quota, please check your plan and billing details. For more information on this error, head to: https://ai.google.dev/gemini-api/docs/rate-limits."},"pid":110158} {"timestamp":"2025-06-25 17:55:17","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"gemini","chunks_processed":1},"pid":110158} {"timestamp":"2025-06-25 17:55:17","session_id":"20250625_173119","level":"ERROR","message":"No valid responses received","context":{"provider":"gemini","chunks_attempted":1},"pid":110158} {"timestamp":"2025-06-25 17:55:17","session_id":"20250625_173119","level":"INFO","message":"API call completed: gemini/gemini-1.5-pro (0.058s)","context":{"provider":"gemini","model":"gemini-1.5-pro","duration_seconds":0.058,"success":true,"tokens":{},"call_count":94},"pid":110158}
{"timestamp":"2025-06-25 17:55:17","session_id":"20250625_173119","level":"INFO","message":"API call completed: gemini/gemini-1.5-pro (0.060s)","context":{"provider":"gemini","model":"gemini-1.5-pro","duration_seconds":0.06,"success":true,"tokens":{},"call_count":95},"pid":110158}
{"timestamp":"2025-06-25 17:55:17","session_id":"20250625_173119","level":"INFO","message":"Model response received successfully","context":{"provider":"gemini","model":"gemini-1.5-pro","response_length":25,"duration_seconds":0.06},"pid":110158}
{"timestamp":"2025-06-25 17:55:17","session_id":"20250625_173119","level":"INFO","message":"Discussion prediction for cluster 9","context":{"cluster_id":"9","event_type":"prediction","data":{"model":"gemini-1.5-pro","round":1,"prediction":"Error: No valid responses"}},"pid":110158}
{"timestamp":"2025-06-25 17:55:17","session_id":"20250625_173119","level":"INFO","message":"Initialized grok processor","context":{"provider":"grok"},"pid":110158}
{"timestamp":"2025-06-25 17:55:17","session_id":"20250625_173119","level":"INFO","message":"Starting grok API request","context":{"model":"grok-3-latest","provider":"grok"},"pid":110158} {"timestamp":"2025-06-25 17:55:17","session_id":"20250625_173119","level":"ERROR","message":"Failed to process chunk 1: $ operator is invalid for atomic vectors","context":{"provider":"grok","model":"grok-3-latest","chunk":1,"error":"$ operator is invalid for atomic vectors"},"pid":110158} {"timestamp":"2025-06-25 17:55:17","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"grok","chunks_processed":1},"pid":110158} {"timestamp":"2025-06-25 17:55:17","session_id":"20250625_173119","level":"ERROR","message":"No valid responses received","context":{"provider":"grok","chunks_attempted":1},"pid":110158} {"timestamp":"2025-06-25 17:55:17","session_id":"20250625_173119","level":"INFO","message":"API call completed: grok/grok-3-latest (0.108s)","context":{"provider":"grok","model":"grok-3-latest","duration_seconds":0.108,"success":true,"tokens":{},"call_count":96},"pid":110158}
{"timestamp":"2025-06-25 17:55:17","session_id":"20250625_173119","level":"INFO","message":"API call completed: grok/grok-3-latest (0.110s)","context":{"provider":"grok","model":"grok-3-latest","duration_seconds":0.11,"success":true,"tokens":{},"call_count":97},"pid":110158}
{"timestamp":"2025-06-25 17:55:17","session_id":"20250625_173119","level":"INFO","message":"Model response received successfully","context":{"provider":"grok","model":"grok-3-latest","response_length":25,"duration_seconds":0.11},"pid":110158}
{"timestamp":"2025-06-25 17:55:17","session_id":"20250625_173119","level":"INFO","message":"Discussion prediction for cluster 9","context":{"cluster_id":"9","event_type":"prediction","data":{"model":"grok-3-latest","round":1,"prediction":"Error: No valid responses"}},"pid":110158}
{"timestamp":"2025-06-25 17:55:17","session_id":"20250625_173119","level":"INFO","message":"Initialized anthropic processor","context":{"provider":"anthropic"},"pid":110158}
{"timestamp":"2025-06-25 17:55:17","session_id":"20250625_173119","level":"INFO","message":"Starting anthropic API request","context":{"model":"claude-3-7-sonnet-20250219","provider":"anthropic"},"pid":110158} {"timestamp":"2025-06-25 17:55:17","session_id":"20250625_173119","level":"ERROR","message":"Anthropic API request failed","context":{"provider":"anthropic","model":"claude-3-7-sonnet-20250219","status_code":400,"error":"Your credit balance is too low to access the Anthropic API. Please go to Plans & Billing to upgrade or purchase credits."},"pid":110158}
{"timestamp":"2025-06-25 17:55:17","session_id":"20250625_173119","level":"ERROR","message":"Failed to process chunk 1: Anthropic API request failed: Your credit balance is too low to access the Anthropic API. Please go to Plans & Billing to upgrade or purchase credits.","context":{"provider":"anthropic","model":"claude-3-7-sonnet-20250219","chunk":1,"error":"Anthropic API request failed: Your credit balance is too low to access the Anthropic API. Please go to Plans & Billing to upgrade or purchase credits."},"pid":110158} {"timestamp":"2025-06-25 17:55:17","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"anthropic","chunks_processed":1},"pid":110158} {"timestamp":"2025-06-25 17:55:17","session_id":"20250625_173119","level":"ERROR","message":"No valid responses received","context":{"provider":"anthropic","chunks_attempted":1},"pid":110158} {"timestamp":"2025-06-25 17:55:17","session_id":"20250625_173119","level":"INFO","message":"API call completed: anthropic/claude-3-7-sonnet-20250219 (0.151s)","context":{"provider":"anthropic","model":"claude-3-7-sonnet-20250219","duration_seconds":0.151,"success":true,"tokens":{},"call_count":98},"pid":110158}
{"timestamp":"2025-06-25 17:55:17","session_id":"20250625_173119","level":"INFO","message":"API call completed: anthropic/claude-3-7-sonnet-20250219 (0.152s)","context":{"provider":"anthropic","model":"claude-3-7-sonnet-20250219","duration_seconds":0.152,"success":true,"tokens":{},"call_count":99},"pid":110158}
{"timestamp":"2025-06-25 17:55:17","session_id":"20250625_173119","level":"INFO","message":"Model response received successfully","context":{"provider":"anthropic","model":"claude-3-7-sonnet-20250219","response_length":25,"duration_seconds":0.152},"pid":110158}
{"timestamp":"2025-06-25 17:55:17","session_id":"20250625_173119","level":"INFO","message":"Discussion prediction for cluster 9","context":{"cluster_id":"9","event_type":"prediction","data":{"model":"claude-3-7-sonnet-20250219","round":1,"prediction":"Error: No valid responses"}},"pid":110158}
{"timestamp":"2025-06-25 17:55:17","session_id":"20250625_173119","level":"INFO","message":"Initialized openai processor","context":{"provider":"openai"},"pid":110158}
{"timestamp":"2025-06-25 17:55:17","session_id":"20250625_173119","level":"INFO","message":"Starting openai API request","context":{"model":"gpt-4o","provider":"openai"},"pid":110158} {"timestamp":"2025-06-25 17:55:17","session_id":"20250625_173119","level":"ERROR","message":"OpenAI API request failed","context":{"error":"You exceeded your current quota, please check your plan and billing details. For more information on this error, read the docs: https://platform.openai.com/docs/guides/error-codes/api-errors.","provider":"openai","model":"gpt-4o","status_code":429},"pid":110158}
{"timestamp":"2025-06-25 17:55:17","session_id":"20250625_173119","level":"ERROR","message":"Failed to process chunk 1: OpenAI API request failed: You exceeded your current quota, please check your plan and billing details. For more information on this error, read the docs: https://platform.openai.com/docs/guides/error-codes/api-errors.","context":{"provider":"openai","model":"gpt-4o","chunk":1,"error":"OpenAI API request failed: You exceeded your current quota, please check your plan and billing details. For more information on this error, read the docs: https://platform.openai.com/docs/guides/error-codes/api-errors."},"pid":110158} {"timestamp":"2025-06-25 17:55:17","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"openai","chunks_processed":1},"pid":110158} {"timestamp":"2025-06-25 17:55:17","session_id":"20250625_173119","level":"ERROR","message":"No valid responses received","context":{"provider":"openai","chunks_attempted":1},"pid":110158} {"timestamp":"2025-06-25 17:55:17","session_id":"20250625_173119","level":"INFO","message":"API call completed: openai/gpt-4o (0.337s)","context":{"provider":"openai","model":"gpt-4o","duration_seconds":0.337,"success":true,"tokens":{},"call_count":100},"pid":110158}
{"timestamp":"2025-06-25 17:55:17","session_id":"20250625_173119","level":"INFO","message":"API call completed: openai/gpt-4o (0.338s)","context":{"provider":"openai","model":"gpt-4o","duration_seconds":0.338,"success":true,"tokens":{},"call_count":101},"pid":110158}
{"timestamp":"2025-06-25 17:55:17","session_id":"20250625_173119","level":"INFO","message":"Model response received successfully","context":{"provider":"openai","model":"gpt-4o","response_length":25,"duration_seconds":0.338},"pid":110158}
{"timestamp":"2025-06-25 17:55:17","session_id":"20250625_173119","level":"INFO","message":"Discussion prediction for cluster 9","context":{"cluster_id":"9","event_type":"prediction","data":{"model":"gpt-4o","round":1,"prediction":"Error: No valid responses"}},"pid":110158}
{"timestamp":"2025-06-25 17:55:17","session_id":"20250625_173119","level":"WARN","message":"Model gemini-2.0-flash failed to provide valid response for cluster 9","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:55:17","session_id":"20250625_173119","level":"WARN","message":"Model gemini-1.5-pro failed to provide valid response for cluster 9","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:55:17","session_id":"20250625_173119","level":"WARN","message":"Model grok-3-latest failed to provide valid response for cluster 9","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:55:17","session_id":"20250625_173119","level":"WARN","message":"Model claude-3-7-sonnet-20250219 failed to provide valid response for cluster 9","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:55:17","session_id":"20250625_173119","level":"WARN","message":"Model gpt-4o failed to provide valid response for cluster 9","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:55:17","session_id":"20250625_173119","level":"WARN","message":"Only 0 valid responses received for cluster 9. Skipping discussion.","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:55:17","session_id":"20250625_173119","level":"INFO","message":"Saved result to cache for cluster 9","context":{"cluster_id":"9"},"pid":110158}
{"timestamp":"2025-06-25 17:55:17","session_id":"20250625_173119","level":"INFO","message":"Completed discussion for cluster 9","context":{"cluster_id":"9"},"pid":110158} Completed discussion for cluster 9{"timestamp":"2025-06-25 17:55:17","session_id":"20250625_173119","level":"INFO","message":"Starting discussion for cluster 10...","context":{"cluster_id":"10"},"pid":110158}
Starting discussion for cluster 10...{"timestamp":"2025-06-25 17:55:17","session_id":"20250625_173119","level":"INFO","message":"Discussion start for cluster 10","context":{"cluster_id":"10","event_type":"start","data":{"tissue_name":"human blood CD4 T cells","marker_genes":"RPS4Y1,IL7R,GIMAP5,GIMAP7,TCF7,GIMAP4,KLF2,PBXIP1,LINC00861,GIMAP1"}},"pid":110158}
{"timestamp":"2025-06-25 17:55:17","session_id":"20250625_173119","level":"INFO","message":"Initialized gemini processor","context":{"provider":"gemini"},"pid":110158}
{"timestamp":"2025-06-25 17:55:17","session_id":"20250625_173119","level":"INFO","message":"Starting gemini API request","context":{"model":"gemini-2.0-flash","provider":"gemini"},"pid":110158}
{"timestamp":"2025-06-25 17:55:25","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"gemini","chunks_processed":1},"pid":110158}
{"timestamp":"2025-06-25 17:55:25","session_id":"20250625_173119","level":"INFO","message":"Results consolidated successfully","context":{"provider":"gemini","valid_chunks":1,"total_lines":20},"pid":110158}
{"timestamp":"2025-06-25 17:55:25","session_id":"20250625_173119","level":"INFO","message":"API call completed: gemini/gemini-2.0-flash (7.688s)","context":{"provider":"gemini","model":"gemini-2.0-flash","duration_seconds":7.688,"success":true,"tokens":{},"call_count":102},"pid":110158}
{"timestamp":"2025-06-25 17:55:25","session_id":"20250625_173119","level":"INFO","message":"API call completed: gemini/gemini-2.0-flash (7.690s)","context":{"provider":"gemini","model":"gemini-2.0-flash","duration_seconds":7.69,"success":true,"tokens":{},"call_count":103},"pid":110158}
{"timestamp":"2025-06-25 17:55:25","session_id":"20250625_173119","level":"INFO","message":"Model response received successfully","context":{"provider":"gemini","model":"gemini-2.0-flash","response_length":[93,0,39,0,115,0,560,0,12,125,153,270,256,128,93,164,0,156,0,985],"duration_seconds":7.69},"pid":110158}
{"timestamp":"2025-06-25 17:55:25","session_id":"20250625_173119","level":"INFO","message":"Discussion prediction for cluster 10","context":{"cluster_id":"10","event_type":"prediction","data":{"model":"gemini-2.0-flash","round":1,"prediction":["Okay, here's my cell type prediction and justification using the Toulmin argumentation model:","","**CELL TYPE:** Naive CD4 T cells (Male)","","**GROUNDS:** The cluster expresses RPS4Y1, IL7R, GIMAP5, GIMAP7, TCF7, GIMAP4, KLF2, PBXIP1, LINC00861, and GIMAP1.","","**WARRANT:** The co-expression of IL7R, TCF7, KLF2, GIMAP family genes (GIMAP1, GIMAP4, GIMAP5, GIMAP7), and PBXIP1 strongly suggests a naive T cell phenotype. IL7R is a receptor for IL-7, crucial for naive T cell survival. TCF7 and KLF2 are transcription factors important for naive T cell identity and homing to lymph nodes. GIMAP family genes are associated with lymphocyte survival and development, particularly in naive T cells. The presence of RPS4Y1 indicates a male origin of the cells. LINC00861 has been implicated in T cell development and function.","","**BACKING:**","* **IL7R:** Interleukin-7 receptor is essential for naive T cell survival and homeostasis. (Fry and Mackall, *Blood*, 2005)","* **TCF7:** Transcription factor 7 (TCF7) is a key regulator of T cell development and naive T cell identity. (Weber et al., *Nature Immunology*, 2011)","* **KLF2:** Krüppel-like factor 2 (KLF2) regulates the expression of sphingosine-1-phosphate receptor 1 (S1PR1), which is essential for T cell egress from lymphoid organs and recirculation, a characteristic of naive T cells. (Allende et al., *Nature Immunology*, 2004)","* **GIMAP family:** GTPase, IMAP family member genes (GIMAPs) are implicated in lymphocyte survival and apoptosis, and their expression is often high in naive T cells. (Kruckenhauser et al., *Immunology*, 2009; Kühn et al., *Journal of Immunology*, 2004)","* **PBXIP1:** Functions in T cell development and differentiation. (Agata, Y., & Shimizu, A. *International Immunology*, 2007)","* **RPS4Y1:** Ribosomal protein S4, Y-linked 1. A Y chromosome gene, indicates male origin.","* **LINC00861:** LINC00861 expression is associated with T cell function and differentiation processes. (cite relevant studies from literature search if available)","","**QUALIFIER:** Highly probable. The combination of these markers provides strong evidence for a naive CD4 T cell phenotype, especially in a male individual.","","**REBUTTAL:** While other models (gemini-1.5-pro, grok-3-latest, claude-3-7-sonnet-20250219, and gpt-4o) provided no prediction, gemini-2.0-flash agrees with the naive T cell classification. The absence of prediction from the other models may be due to differences in their training data or algorithm. The presence of multiple genes strongly associated with naive T cell identity and survival makes the naive T cell classification the most compelling. However, without functional assays (e.g., assessing cytokine production after stimulation), we cannot definitively exclude the possibility of a transitional or early memory T cell population that retains some naive markers. The high expression of GIMAP genes is very characteristic of naive T cells, reducing the likelihood of this being a memory population. Also, it's important to consider that gene expression profiles can vary depending on the specific experimental conditions and the platform used for measuring gene expression."]}},"pid":110158}
{"timestamp":"2025-06-25 17:55:25","session_id":"20250625_173119","level":"INFO","message":"Initialized gemini processor","context":{"provider":"gemini"},"pid":110158}
{"timestamp":"2025-06-25 17:55:25","session_id":"20250625_173119","level":"INFO","message":"Starting gemini API request","context":{"model":"gemini-1.5-pro","provider":"gemini"},"pid":110158} {"timestamp":"2025-06-25 17:55:25","session_id":"20250625_173119","level":"ERROR","message":"Gemini API request failed","context":{"error":"You exceeded your current quota, please check your plan and billing details. For more information on this error, head to: https://ai.google.dev/gemini-api/docs/rate-limits.","provider":"gemini","model":"gemini-1.5-pro","status_code":429},"pid":110158}
{"timestamp":"2025-06-25 17:55:25","session_id":"20250625_173119","level":"ERROR","message":"Failed to process chunk 1: Gemini API request failed: You exceeded your current quota, please check your plan and billing details. For more information on this error, head to: https://ai.google.dev/gemini-api/docs/rate-limits.","context":{"provider":"gemini","model":"gemini-1.5-pro","chunk":1,"error":"Gemini API request failed: You exceeded your current quota, please check your plan and billing details. For more information on this error, head to: https://ai.google.dev/gemini-api/docs/rate-limits."},"pid":110158} {"timestamp":"2025-06-25 17:55:25","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"gemini","chunks_processed":1},"pid":110158} {"timestamp":"2025-06-25 17:55:25","session_id":"20250625_173119","level":"ERROR","message":"No valid responses received","context":{"provider":"gemini","chunks_attempted":1},"pid":110158} {"timestamp":"2025-06-25 17:55:25","session_id":"20250625_173119","level":"INFO","message":"API call completed: gemini/gemini-1.5-pro (0.049s)","context":{"provider":"gemini","model":"gemini-1.5-pro","duration_seconds":0.049,"success":true,"tokens":{},"call_count":104},"pid":110158}
{"timestamp":"2025-06-25 17:55:25","session_id":"20250625_173119","level":"INFO","message":"API call completed: gemini/gemini-1.5-pro (0.051s)","context":{"provider":"gemini","model":"gemini-1.5-pro","duration_seconds":0.051,"success":true,"tokens":{},"call_count":105},"pid":110158}
{"timestamp":"2025-06-25 17:55:25","session_id":"20250625_173119","level":"INFO","message":"Model response received successfully","context":{"provider":"gemini","model":"gemini-1.5-pro","response_length":25,"duration_seconds":0.051},"pid":110158}
{"timestamp":"2025-06-25 17:55:25","session_id":"20250625_173119","level":"INFO","message":"Discussion prediction for cluster 10","context":{"cluster_id":"10","event_type":"prediction","data":{"model":"gemini-1.5-pro","round":1,"prediction":"Error: No valid responses"}},"pid":110158}
{"timestamp":"2025-06-25 17:55:25","session_id":"20250625_173119","level":"INFO","message":"Initialized grok processor","context":{"provider":"grok"},"pid":110158}
{"timestamp":"2025-06-25 17:55:25","session_id":"20250625_173119","level":"INFO","message":"Starting grok API request","context":{"model":"grok-3-latest","provider":"grok"},"pid":110158} {"timestamp":"2025-06-25 17:55:25","session_id":"20250625_173119","level":"ERROR","message":"Failed to process chunk 1: $ operator is invalid for atomic vectors","context":{"provider":"grok","model":"grok-3-latest","chunk":1,"error":"$ operator is invalid for atomic vectors"},"pid":110158} {"timestamp":"2025-06-25 17:55:25","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"grok","chunks_processed":1},"pid":110158} {"timestamp":"2025-06-25 17:55:25","session_id":"20250625_173119","level":"ERROR","message":"No valid responses received","context":{"provider":"grok","chunks_attempted":1},"pid":110158} {"timestamp":"2025-06-25 17:55:25","session_id":"20250625_173119","level":"INFO","message":"API call completed: grok/grok-3-latest (0.127s)","context":{"provider":"grok","model":"grok-3-latest","duration_seconds":0.127,"success":true,"tokens":{},"call_count":106},"pid":110158}
{"timestamp":"2025-06-25 17:55:25","session_id":"20250625_173119","level":"INFO","message":"API call completed: grok/grok-3-latest (0.129s)","context":{"provider":"grok","model":"grok-3-latest","duration_seconds":0.129,"success":true,"tokens":{},"call_count":107},"pid":110158}
{"timestamp":"2025-06-25 17:55:25","session_id":"20250625_173119","level":"INFO","message":"Model response received successfully","context":{"provider":"grok","model":"grok-3-latest","response_length":25,"duration_seconds":0.129},"pid":110158}
{"timestamp":"2025-06-25 17:55:25","session_id":"20250625_173119","level":"INFO","message":"Discussion prediction for cluster 10","context":{"cluster_id":"10","event_type":"prediction","data":{"model":"grok-3-latest","round":1,"prediction":"Error: No valid responses"}},"pid":110158}
{"timestamp":"2025-06-25 17:55:25","session_id":"20250625_173119","level":"INFO","message":"Initialized anthropic processor","context":{"provider":"anthropic"},"pid":110158}
{"timestamp":"2025-06-25 17:55:25","session_id":"20250625_173119","level":"INFO","message":"Starting anthropic API request","context":{"model":"claude-3-7-sonnet-20250219","provider":"anthropic"},"pid":110158} {"timestamp":"2025-06-25 17:55:25","session_id":"20250625_173119","level":"ERROR","message":"Anthropic API request failed","context":{"provider":"anthropic","model":"claude-3-7-sonnet-20250219","status_code":400,"error":"Your credit balance is too low to access the Anthropic API. Please go to Plans & Billing to upgrade or purchase credits."},"pid":110158}
{"timestamp":"2025-06-25 17:55:25","session_id":"20250625_173119","level":"ERROR","message":"Failed to process chunk 1: Anthropic API request failed: Your credit balance is too low to access the Anthropic API. Please go to Plans & Billing to upgrade or purchase credits.","context":{"provider":"anthropic","model":"claude-3-7-sonnet-20250219","chunk":1,"error":"Anthropic API request failed: Your credit balance is too low to access the Anthropic API. Please go to Plans & Billing to upgrade or purchase credits."},"pid":110158} {"timestamp":"2025-06-25 17:55:25","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"anthropic","chunks_processed":1},"pid":110158} {"timestamp":"2025-06-25 17:55:25","session_id":"20250625_173119","level":"ERROR","message":"No valid responses received","context":{"provider":"anthropic","chunks_attempted":1},"pid":110158} {"timestamp":"2025-06-25 17:55:25","session_id":"20250625_173119","level":"INFO","message":"API call completed: anthropic/claude-3-7-sonnet-20250219 (0.155s)","context":{"provider":"anthropic","model":"claude-3-7-sonnet-20250219","duration_seconds":0.155,"success":true,"tokens":{},"call_count":108},"pid":110158}
{"timestamp":"2025-06-25 17:55:25","session_id":"20250625_173119","level":"INFO","message":"API call completed: anthropic/claude-3-7-sonnet-20250219 (0.157s)","context":{"provider":"anthropic","model":"claude-3-7-sonnet-20250219","duration_seconds":0.157,"success":true,"tokens":{},"call_count":109},"pid":110158}
{"timestamp":"2025-06-25 17:55:25","session_id":"20250625_173119","level":"INFO","message":"Model response received successfully","context":{"provider":"anthropic","model":"claude-3-7-sonnet-20250219","response_length":25,"duration_seconds":0.157},"pid":110158}
{"timestamp":"2025-06-25 17:55:25","session_id":"20250625_173119","level":"INFO","message":"Discussion prediction for cluster 10","context":{"cluster_id":"10","event_type":"prediction","data":{"model":"claude-3-7-sonnet-20250219","round":1,"prediction":"Error: No valid responses"}},"pid":110158}
{"timestamp":"2025-06-25 17:55:25","session_id":"20250625_173119","level":"INFO","message":"Initialized openai processor","context":{"provider":"openai"},"pid":110158}
{"timestamp":"2025-06-25 17:55:25","session_id":"20250625_173119","level":"INFO","message":"Starting openai API request","context":{"model":"gpt-4o","provider":"openai"},"pid":110158} {"timestamp":"2025-06-25 17:55:25","session_id":"20250625_173119","level":"ERROR","message":"OpenAI API request failed","context":{"error":"You exceeded your current quota, please check your plan and billing details. For more information on this error, read the docs: https://platform.openai.com/docs/guides/error-codes/api-errors.","provider":"openai","model":"gpt-4o","status_code":429},"pid":110158}
{"timestamp":"2025-06-25 17:55:25","session_id":"20250625_173119","level":"ERROR","message":"Failed to process chunk 1: OpenAI API request failed: You exceeded your current quota, please check your plan and billing details. For more information on this error, read the docs: https://platform.openai.com/docs/guides/error-codes/api-errors.","context":{"provider":"openai","model":"gpt-4o","chunk":1,"error":"OpenAI API request failed: You exceeded your current quota, please check your plan and billing details. For more information on this error, read the docs: https://platform.openai.com/docs/guides/error-codes/api-errors."},"pid":110158} {"timestamp":"2025-06-25 17:55:25","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"openai","chunks_processed":1},"pid":110158} {"timestamp":"2025-06-25 17:55:25","session_id":"20250625_173119","level":"ERROR","message":"No valid responses received","context":{"provider":"openai","chunks_attempted":1},"pid":110158} {"timestamp":"2025-06-25 17:55:25","session_id":"20250625_173119","level":"INFO","message":"API call completed: openai/gpt-4o (0.169s)","context":{"provider":"openai","model":"gpt-4o","duration_seconds":0.169,"success":true,"tokens":{},"call_count":110},"pid":110158}
{"timestamp":"2025-06-25 17:55:25","session_id":"20250625_173119","level":"INFO","message":"API call completed: openai/gpt-4o (0.170s)","context":{"provider":"openai","model":"gpt-4o","duration_seconds":0.17,"success":true,"tokens":{},"call_count":111},"pid":110158}
{"timestamp":"2025-06-25 17:55:25","session_id":"20250625_173119","level":"INFO","message":"Model response received successfully","context":{"provider":"openai","model":"gpt-4o","response_length":25,"duration_seconds":0.17},"pid":110158}
{"timestamp":"2025-06-25 17:55:25","session_id":"20250625_173119","level":"INFO","message":"Discussion prediction for cluster 10","context":{"cluster_id":"10","event_type":"prediction","data":{"model":"gpt-4o","round":1,"prediction":"Error: No valid responses"}},"pid":110158}
{"timestamp":"2025-06-25 17:55:25","session_id":"20250625_173119","level":"WARN","message":"Model gemini-1.5-pro failed to provide valid response for cluster 10","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:55:25","session_id":"20250625_173119","level":"WARN","message":"Model grok-3-latest failed to provide valid response for cluster 10","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:55:25","session_id":"20250625_173119","level":"WARN","message":"Model claude-3-7-sonnet-20250219 failed to provide valid response for cluster 10","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:55:25","session_id":"20250625_173119","level":"WARN","message":"Model gpt-4o failed to provide valid response for cluster 10","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:55:25","session_id":"20250625_173119","level":"WARN","message":"Only 1 valid responses received for cluster 10. Skipping discussion.","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:55:25","session_id":"20250625_173119","level":"INFO","message":"Saved result to cache for cluster 10","context":{"cluster_id":"10"},"pid":110158}
{"timestamp":"2025-06-25 17:55:25","session_id":"20250625_173119","level":"INFO","message":"Completed discussion for cluster 10","context":{"cluster_id":"10"},"pid":110158} Completed discussion for cluster 10{"timestamp":"2025-06-25 17:55:25","session_id":"20250625_173119","level":"INFO","message":"Starting discussion for cluster 11...","context":{"cluster_id":"11"},"pid":110158}
Starting discussion for cluster 11...{"timestamp":"2025-06-25 17:55:25","session_id":"20250625_173119","level":"INFO","message":"Discussion start for cluster 11","context":{"cluster_id":"11","event_type":"start","data":{"tissue_name":"human blood CD4 T cells","marker_genes":"CD52,TRBV20-1,LAPTM5,SOCS1,S100A4,S100A11,FXYD5,SH3BGRL3,S100A6,IL32"}},"pid":110158}
{"timestamp":"2025-06-25 17:55:25","session_id":"20250625_173119","level":"INFO","message":"Initialized gemini processor","context":{"provider":"gemini"},"pid":110158}
{"timestamp":"2025-06-25 17:55:25","session_id":"20250625_173119","level":"INFO","message":"Starting gemini API request","context":{"model":"gemini-2.0-flash","provider":"gemini"},"pid":110158}
{"timestamp":"2025-06-25 17:55:33","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"gemini","chunks_processed":1},"pid":110158}
{"timestamp":"2025-06-25 17:55:33","session_id":"20250625_173119","level":"INFO","message":"Results consolidated successfully","context":{"provider":"gemini","valid_chunks":1,"total_lines":23},"pid":110158}
{"timestamp":"2025-06-25 17:55:33","session_id":"20250625_173119","level":"INFO","message":"API call completed: gemini/gemini-2.0-flash (8.035s)","context":{"provider":"gemini","model":"gemini-2.0-flash","duration_seconds":8.035,"success":true,"tokens":{},"call_count":112},"pid":110158}
{"timestamp":"2025-06-25 17:55:33","session_id":"20250625_173119","level":"INFO","message":"API call completed: gemini/gemini-2.0-flash (8.037s)","context":{"provider":"gemini","model":"gemini-2.0-flash","duration_seconds":8.037,"success":true,"tokens":{},"call_count":113},"pid":110158}
{"timestamp":"2025-06-25 17:55:33","session_id":"20250625_173119","level":"INFO","message":"Model response received successfully","context":{"provider":"gemini","model":"gemini-2.0-flash","response_length":[52,0,113,0,997,0,8,96,172,258,394,258,259,181,157,150,140,166,168,0,351,0,790],"duration_seconds":8.037},"pid":110158}
{"timestamp":"2025-06-25 17:55:33","session_id":"20250625_173119","level":"INFO","message":"Discussion prediction for cluster 11","context":{"cluster_id":"11","event_type":"prediction","data":{"model":"gemini-2.0-flash","round":1,"prediction":["CELL TYPE: **Activated/Effector Memory CD4+ T cell**","","GROUNDS: The cluster expresses CD52, TRBV20-1, LAPTM5, SOCS1, S100A4, S100A11, FXYD5, SH3BGRL3, S100A6, and IL32.","","WARRANT: This specific gene expression profile points to activated/effector memory CD4+ T cells. CD52 is broadly expressed in T cells, but its presence indicates T cell lineage. The presence of TRBV20-1 suggests a specific T cell receptor rearrangement, indicating antigen experience. Genes related to activation, such as SOCS1 and IL32, coupled with genes associated with migration and effector function (S100A4, S100A6, S100A11), are characteristic of cells that have been stimulated and are ready to perform their immune functions. LAPTM5 expression can be indicative of lysosomal activity in immune cells, supporting effector function. FXYD5 and SH3BGRL3 may also contribute to T cell function, although their specific roles are less well-defined in the context of CD4+ T cell activation. The S100 family genes (S100A4, S100A6, S100A11) are frequently associated with inflammation and migration, further suggesting an activated and potentially tissue-resident effector memory T cell phenotype.","","BACKING:","* **CD52:** Expressed on mature lymphocytes, including CD4+ T cells (Hale, G. *et al.*, 1990).","* **IL32:** Is a pro-inflammatory cytokine expressed by activated T cells (Kim, S. H. *et al.*, 2005). It's associated with T cell activation and inflammatory conditions.","* **SOCS1:** Is a negative regulator of cytokine signaling. Expression is often upregulated following T cell activation to prevent excessive inflammation (Yoshimura, A. *et al.*, 2004). Its presence suggests the cells have experienced activation signaling.","* **S100A4, S100A6, S100A11:** These S100 proteins are calcium-binding proteins often involved in cell migration, inflammation, and metastasis. Their expression in T cells has been linked to effector functions and migration to sites of inflammation (Boye, T. L. *et al.*, 2017). In particular, S100A4 is a marker of T cell activation and is involved in T cell migration and tissue remodeling.","* **LAPTM5:** Involved in lysosomal function and turnover of surface proteins. Highly expressed in hematopoietic cells and modulates immune responses (Winkler, K. *et al.*, 2009). This supports effector function through antigen processing and presentation.","* **TRBV20-1:** Represents a specific T cell receptor beta variable chain usage. While it doesn't define a cell type *per se*, its presence indicates an antigen-experienced cell that has undergone clonal expansion after interacting with its cognate antigen.","* **FXYD5 and SH3BGRL3:** While less specific, can be expressed in T cells; functional roles less defined but suggest involvement in signalling and adaptation to microenvironment.","* Hale, G., Clark, M. R., & Waldmann, H. (1990). Therapeutic potential of Campath-1: isotype selection studies. *Journal of Immunology*, *144*(4), 1394-1400.","* Kim, S. H., Azam, T., Yoon, D. Y., & Dinarello, C. A. (2005). IL-32: a novel proinflammatory cytokine. *Journal of Immunology*, *175*(3), 1917-1924.","* Yoshimura, A., Naka, T., & Kubo, M. (2004). SOCS proteins, cytokine signalling and immunity. *Nature Reviews Immunology*, *4*(3), 216-227.","* Boye, T. L., Christensen, K. L., Jensen, O. N., & Thor Straten, P. (2017). S100A4 is an independent marker of T cell activation. *OncoImmunology*, *6*(8), e1339294.","* Winkler, K., Sommer, U., Sytkowski, A., & Einsele, H. (2009). LAPTM5 is expressed in hematopoietic cells and modulates immune responses. *Leukemia*, *23*(1), 151-158.","","QUALIFIER: Probable. While the gene expression profile is strongly suggestive of activated/effector memory CD4+ T cells, further characterization, such as flow cytometry analysis for cell surface markers (e.g., CD45RO, CD45RA, CD69, CD103), or functional assays (e.g., cytokine secretion upon stimulation), would be needed for definitive confirmation.","","REBUTTAL: While some models predicted \"No prediction,\" the presented marker gene profile strongly supports the prediction of activated/effector memory CD4+ T cells. A lack of a prediction from other models doesn't invalidate the claim, but rather indicates a lower confidence level or a difference in the model's interpretation of the data. It is possible that some of the genes expressed could also be found in other T cell subsets, such as regulatory T cells in specific activation states, but the combination of activation markers, effector function markers, and S100 proteins shifts the likelihood towards the activated/effector memory phenotype. Further, while the individual role of FXYD5 and SH3BGRL3 in T cells needs more definition, they don't negate the other more telling marker."]}},"pid":110158}
{"timestamp":"2025-06-25 17:55:33","session_id":"20250625_173119","level":"INFO","message":"Initialized gemini processor","context":{"provider":"gemini"},"pid":110158}
{"timestamp":"2025-06-25 17:55:33","session_id":"20250625_173119","level":"INFO","message":"Starting gemini API request","context":{"model":"gemini-1.5-pro","provider":"gemini"},"pid":110158} {"timestamp":"2025-06-25 17:55:34","session_id":"20250625_173119","level":"ERROR","message":"Gemini API request failed","context":{"error":"You exceeded your current quota, please check your plan and billing details. For more information on this error, head to: https://ai.google.dev/gemini-api/docs/rate-limits.","provider":"gemini","model":"gemini-1.5-pro","status_code":429},"pid":110158}
{"timestamp":"2025-06-25 17:55:34","session_id":"20250625_173119","level":"ERROR","message":"Failed to process chunk 1: Gemini API request failed: You exceeded your current quota, please check your plan and billing details. For more information on this error, head to: https://ai.google.dev/gemini-api/docs/rate-limits.","context":{"provider":"gemini","model":"gemini-1.5-pro","chunk":1,"error":"Gemini API request failed: You exceeded your current quota, please check your plan and billing details. For more information on this error, head to: https://ai.google.dev/gemini-api/docs/rate-limits."},"pid":110158} {"timestamp":"2025-06-25 17:55:34","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"gemini","chunks_processed":1},"pid":110158} {"timestamp":"2025-06-25 17:55:34","session_id":"20250625_173119","level":"ERROR","message":"No valid responses received","context":{"provider":"gemini","chunks_attempted":1},"pid":110158} {"timestamp":"2025-06-25 17:55:34","session_id":"20250625_173119","level":"INFO","message":"API call completed: gemini/gemini-1.5-pro (0.062s)","context":{"provider":"gemini","model":"gemini-1.5-pro","duration_seconds":0.062,"success":true,"tokens":{},"call_count":114},"pid":110158}
{"timestamp":"2025-06-25 17:55:34","session_id":"20250625_173119","level":"INFO","message":"API call completed: gemini/gemini-1.5-pro (0.064s)","context":{"provider":"gemini","model":"gemini-1.5-pro","duration_seconds":0.064,"success":true,"tokens":{},"call_count":115},"pid":110158}
{"timestamp":"2025-06-25 17:55:34","session_id":"20250625_173119","level":"INFO","message":"Model response received successfully","context":{"provider":"gemini","model":"gemini-1.5-pro","response_length":25,"duration_seconds":0.064},"pid":110158}
{"timestamp":"2025-06-25 17:55:34","session_id":"20250625_173119","level":"INFO","message":"Discussion prediction for cluster 11","context":{"cluster_id":"11","event_type":"prediction","data":{"model":"gemini-1.5-pro","round":1,"prediction":"Error: No valid responses"}},"pid":110158}
{"timestamp":"2025-06-25 17:55:34","session_id":"20250625_173119","level":"INFO","message":"Initialized grok processor","context":{"provider":"grok"},"pid":110158}
{"timestamp":"2025-06-25 17:55:34","session_id":"20250625_173119","level":"INFO","message":"Starting grok API request","context":{"model":"grok-3-latest","provider":"grok"},"pid":110158} {"timestamp":"2025-06-25 17:55:34","session_id":"20250625_173119","level":"ERROR","message":"Failed to process chunk 1: $ operator is invalid for atomic vectors","context":{"provider":"grok","model":"grok-3-latest","chunk":1,"error":"$ operator is invalid for atomic vectors"},"pid":110158} {"timestamp":"2025-06-25 17:55:34","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"grok","chunks_processed":1},"pid":110158} {"timestamp":"2025-06-25 17:55:34","session_id":"20250625_173119","level":"ERROR","message":"No valid responses received","context":{"provider":"grok","chunks_attempted":1},"pid":110158} {"timestamp":"2025-06-25 17:55:34","session_id":"20250625_173119","level":"INFO","message":"API call completed: grok/grok-3-latest (0.110s)","context":{"provider":"grok","model":"grok-3-latest","duration_seconds":0.11,"success":true,"tokens":{},"call_count":116},"pid":110158}
{"timestamp":"2025-06-25 17:55:34","session_id":"20250625_173119","level":"INFO","message":"API call completed: grok/grok-3-latest (0.112s)","context":{"provider":"grok","model":"grok-3-latest","duration_seconds":0.112,"success":true,"tokens":{},"call_count":117},"pid":110158}
{"timestamp":"2025-06-25 17:55:34","session_id":"20250625_173119","level":"INFO","message":"Model response received successfully","context":{"provider":"grok","model":"grok-3-latest","response_length":25,"duration_seconds":0.112},"pid":110158}
{"timestamp":"2025-06-25 17:55:34","session_id":"20250625_173119","level":"INFO","message":"Discussion prediction for cluster 11","context":{"cluster_id":"11","event_type":"prediction","data":{"model":"grok-3-latest","round":1,"prediction":"Error: No valid responses"}},"pid":110158}
{"timestamp":"2025-06-25 17:55:34","session_id":"20250625_173119","level":"INFO","message":"Initialized anthropic processor","context":{"provider":"anthropic"},"pid":110158}
{"timestamp":"2025-06-25 17:55:34","session_id":"20250625_173119","level":"INFO","message":"Starting anthropic API request","context":{"model":"claude-3-7-sonnet-20250219","provider":"anthropic"},"pid":110158} {"timestamp":"2025-06-25 17:55:34","session_id":"20250625_173119","level":"ERROR","message":"Anthropic API request failed","context":{"provider":"anthropic","model":"claude-3-7-sonnet-20250219","status_code":400,"error":"Your credit balance is too low to access the Anthropic API. Please go to Plans & Billing to upgrade or purchase credits."},"pid":110158}
{"timestamp":"2025-06-25 17:55:34","session_id":"20250625_173119","level":"ERROR","message":"Failed to process chunk 1: Anthropic API request failed: Your credit balance is too low to access the Anthropic API. Please go to Plans & Billing to upgrade or purchase credits.","context":{"provider":"anthropic","model":"claude-3-7-sonnet-20250219","chunk":1,"error":"Anthropic API request failed: Your credit balance is too low to access the Anthropic API. Please go to Plans & Billing to upgrade or purchase credits."},"pid":110158} {"timestamp":"2025-06-25 17:55:34","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"anthropic","chunks_processed":1},"pid":110158} {"timestamp":"2025-06-25 17:55:34","session_id":"20250625_173119","level":"ERROR","message":"No valid responses received","context":{"provider":"anthropic","chunks_attempted":1},"pid":110158} {"timestamp":"2025-06-25 17:55:34","session_id":"20250625_173119","level":"INFO","message":"API call completed: anthropic/claude-3-7-sonnet-20250219 (0.147s)","context":{"provider":"anthropic","model":"claude-3-7-sonnet-20250219","duration_seconds":0.147,"success":true,"tokens":{},"call_count":118},"pid":110158}
{"timestamp":"2025-06-25 17:55:34","session_id":"20250625_173119","level":"INFO","message":"API call completed: anthropic/claude-3-7-sonnet-20250219 (0.148s)","context":{"provider":"anthropic","model":"claude-3-7-sonnet-20250219","duration_seconds":0.148,"success":true,"tokens":{},"call_count":119},"pid":110158}
{"timestamp":"2025-06-25 17:55:34","session_id":"20250625_173119","level":"INFO","message":"Model response received successfully","context":{"provider":"anthropic","model":"claude-3-7-sonnet-20250219","response_length":25,"duration_seconds":0.148},"pid":110158}
{"timestamp":"2025-06-25 17:55:34","session_id":"20250625_173119","level":"INFO","message":"Discussion prediction for cluster 11","context":{"cluster_id":"11","event_type":"prediction","data":{"model":"claude-3-7-sonnet-20250219","round":1,"prediction":"Error: No valid responses"}},"pid":110158}
{"timestamp":"2025-06-25 17:55:34","session_id":"20250625_173119","level":"INFO","message":"Initialized openai processor","context":{"provider":"openai"},"pid":110158}
{"timestamp":"2025-06-25 17:55:34","session_id":"20250625_173119","level":"INFO","message":"Starting openai API request","context":{"model":"gpt-4o","provider":"openai"},"pid":110158} {"timestamp":"2025-06-25 17:55:34","session_id":"20250625_173119","level":"ERROR","message":"OpenAI API request failed","context":{"error":"You exceeded your current quota, please check your plan and billing details. For more information on this error, read the docs: https://platform.openai.com/docs/guides/error-codes/api-errors.","provider":"openai","model":"gpt-4o","status_code":429},"pid":110158}
{"timestamp":"2025-06-25 17:55:34","session_id":"20250625_173119","level":"ERROR","message":"Failed to process chunk 1: OpenAI API request failed: You exceeded your current quota, please check your plan and billing details. For more information on this error, read the docs: https://platform.openai.com/docs/guides/error-codes/api-errors.","context":{"provider":"openai","model":"gpt-4o","chunk":1,"error":"OpenAI API request failed: You exceeded your current quota, please check your plan and billing details. For more information on this error, read the docs: https://platform.openai.com/docs/guides/error-codes/api-errors."},"pid":110158} {"timestamp":"2025-06-25 17:55:34","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"openai","chunks_processed":1},"pid":110158} {"timestamp":"2025-06-25 17:55:34","session_id":"20250625_173119","level":"ERROR","message":"No valid responses received","context":{"provider":"openai","chunks_attempted":1},"pid":110158} {"timestamp":"2025-06-25 17:55:34","session_id":"20250625_173119","level":"INFO","message":"API call completed: openai/gpt-4o (0.489s)","context":{"provider":"openai","model":"gpt-4o","duration_seconds":0.489,"success":true,"tokens":{},"call_count":120},"pid":110158}
{"timestamp":"2025-06-25 17:55:34","session_id":"20250625_173119","level":"INFO","message":"API call completed: openai/gpt-4o (0.490s)","context":{"provider":"openai","model":"gpt-4o","duration_seconds":0.49,"success":true,"tokens":{},"call_count":121},"pid":110158}
{"timestamp":"2025-06-25 17:55:34","session_id":"20250625_173119","level":"INFO","message":"Model response received successfully","context":{"provider":"openai","model":"gpt-4o","response_length":25,"duration_seconds":0.49},"pid":110158}
{"timestamp":"2025-06-25 17:55:34","session_id":"20250625_173119","level":"INFO","message":"Discussion prediction for cluster 11","context":{"cluster_id":"11","event_type":"prediction","data":{"model":"gpt-4o","round":1,"prediction":"Error: No valid responses"}},"pid":110158}
{"timestamp":"2025-06-25 17:55:34","session_id":"20250625_173119","level":"WARN","message":"Model gemini-1.5-pro failed to provide valid response for cluster 11","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:55:34","session_id":"20250625_173119","level":"WARN","message":"Model grok-3-latest failed to provide valid response for cluster 11","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:55:34","session_id":"20250625_173119","level":"WARN","message":"Model claude-3-7-sonnet-20250219 failed to provide valid response for cluster 11","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:55:34","session_id":"20250625_173119","level":"WARN","message":"Model gpt-4o failed to provide valid response for cluster 11","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:55:34","session_id":"20250625_173119","level":"WARN","message":"Only 1 valid responses received for cluster 11. Skipping discussion.","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:55:34","session_id":"20250625_173119","level":"INFO","message":"Saved result to cache for cluster 11","context":{"cluster_id":"11"},"pid":110158}
{"timestamp":"2025-06-25 17:55:34","session_id":"20250625_173119","level":"INFO","message":"Completed discussion for cluster 11","context":{"cluster_id":"11"},"pid":110158} Completed discussion for cluster 11{"timestamp":"2025-06-25 17:55:34","session_id":"20250625_173119","level":"INFO","message":"Starting discussion for cluster 12...","context":{"cluster_id":"12"},"pid":110158}
Starting discussion for cluster 12...{"timestamp":"2025-06-25 17:55:34","session_id":"20250625_173119","level":"INFO","message":"Discussion start for cluster 12","context":{"cluster_id":"12","event_type":"start","data":{"tissue_name":"human blood CD4 T cells","marker_genes":"DUSP4,TNFSF9,RGS1,AC114977.1,CD40,CCL3,SERPINE1,CSF2,CCL1,GZMB"}},"pid":110158}
{"timestamp":"2025-06-25 17:55:34","session_id":"20250625_173119","level":"INFO","message":"Initialized gemini processor","context":{"provider":"gemini"},"pid":110158}
{"timestamp":"2025-06-25 17:55:34","session_id":"20250625_173119","level":"INFO","message":"Starting gemini API request","context":{"model":"gemini-2.0-flash","provider":"gemini"},"pid":110158}
{"timestamp":"2025-06-25 17:55:41","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"gemini","chunks_processed":1},"pid":110158}
{"timestamp":"2025-06-25 17:55:41","session_id":"20250625_173119","level":"INFO","message":"Results consolidated successfully","context":{"provider":"gemini","valid_chunks":1,"total_lines":17},"pid":110158}
{"timestamp":"2025-06-25 17:55:41","session_id":"20250625_173119","level":"INFO","message":"API call completed: gemini/gemini-2.0-flash (6.794s)","context":{"provider":"gemini","model":"gemini-2.0-flash","duration_seconds":6.794,"success":true,"tokens":{},"call_count":122},"pid":110158}
{"timestamp":"2025-06-25 17:55:41","session_id":"20250625_173119","level":"INFO","message":"API call completed: gemini/gemini-2.0-flash (6.795s)","context":{"provider":"gemini","model":"gemini-2.0-flash","duration_seconds":6.795,"success":true,"tokens":{},"call_count":123},"pid":110158}
{"timestamp":"2025-06-25 17:55:41","session_id":"20250625_173119","level":"INFO","message":"Model response received successfully","context":{"provider":"gemini","model":"gemini-2.0-flash","response_length":[68,0,115,0,879,0,8,234,369,292,574,321,174,0,261,0,840],"duration_seconds":6.795},"pid":110158}
{"timestamp":"2025-06-25 17:55:41","session_id":"20250625_173119","level":"INFO","message":"Discussion prediction for cluster 12","context":{"cluster_id":"12","event_type":"prediction","data":{"model":"gemini-2.0-flash","round":1,"prediction":["CELL TYPE: Activated CD4 T cells, specifically likely Th1-polarized.","","GROUNDS: The cluster expresses DUSP4, TNFSF9 (4-1BB), RGS1, AC114977.1, CD40, CCL3, SERPINE1, CSF2, CCL1, and GZMB.","","WARRANT: The expression of these genes indicates an activated CD4 T cell undergoing proliferation and effector function. CD40, TNFSF9, CSF2, CCL1, CCL3, and GZMB are all associated with T cell activation and Th1 polarization. DUSP4 is a MAP kinase phosphatase involved in regulating T cell signaling pathways, which is commonly upregulated upon activation. SERPINE1 is involved in extracellular matrix remodeling and can be upregulated in activated T cells during tissue inflammation. While RGS1 can be involved in regulating immune cell migration, its presence here doesn't preclude the conclusion of activation. The presence of GZMB (granzyme B) points towards cytotoxic potential in these CD4 T cells, which can occur in Th1 cells. AC114977.1 function is not entirely understood, but its co-expression with other activation markers strengthens the case for an activated state.","","BACKING:","* **CD40 and TNFSF9 (4-1BB):** These are costimulatory molecules that enhance T cell activation, proliferation, and survival. (Watts, T. H. (2005). TNF/TNFR family members in costimulation. *Annual Review of Immunology, 23*, 23–68.)","* **CCL1 and CCL3:** These are chemokines that attract other immune cells, facilitating immune responses. CCL3, in particular, is important for macrophage recruitment and activation, consistent with a Th1 profile. (Mantovani, A., et al. (2004). The chemokine system in diverse forms of macrophage activation and polarization. *Trends in Immunology, 25*(12), 677-686.)","* **CSF2 (GM-CSF):** This cytokine promotes the differentiation and activation of myeloid cells, particularly macrophages and dendritic cells, which are important for Th1 responses. (Hamilton, J. A. (2002). GM-CSF in inflammation and autoimmunity. *Seminars in Immunology, 14*(5), 313-322.)","* **GZMB (Granzyme B):** This serine protease is expressed by cytotoxic lymphocytes, including CD8 T cells and also certain subsets of CD4 T cells (Th1). It mediates target cell apoptosis. (Trapani, J. A., & Smyth, M. J. (2002). Functional significance of the perforin/granzyme cell-mediated cytotoxicity pathway. *Nature Reviews Immunology, 2*(10), 735-747.) Th1 CD4 T cells have been shown to express granzyme B and exhibit cytotoxic activity. (Takeuchi, A., et al. (2018). Functional specializations of cytotoxic CD4+ T lymphocytes. *Frontiers in Immunology, 9*, 2477.)","* **DUSP4:** DUSP4 is a phosphatase that dephosphorylates and inactivates ERK. It has been shown to play a role in regulating T cell activation and differentiation. (Zhang, Z., et al. (2012). The dual-specificity phosphatase DUSP4 negatively regulates T cell activation. *The Journal of Immunology, 188*(6), 2612-2620.)","* **SERPINE1:** Also known as plasminogen activator inhibitor-1 (PAI-1), this gene is induced in activated T cells and can contribute to inflammation and tissue remodeling.","","QUALIFIER: Highly probable. While the presence of all the Th1-related markers is strongly suggestive, definitive confirmation might require further functional assays (e.g., cytokine production) or assessment of intracellular transcription factors (e.g., T-bet).","","REBUTTAL: While several models predicted \"no prediction,\" the gene signature strongly points towards an activated CD4 T cell phenotype. The lack of prediction from the other models may be due to the specific training data used or the inherent limitations of the models in extrapolating complex gene expression patterns to specific cell types. While RGS1's presence could suggest a regulatory function, the overwhelming evidence of the other markers strongly outweighs this possibility in this cluster. The presence of Granzyme B is more commonly associated with CD8 T cells and NK cells. However, it is well-documented that CD4 T cells, especially Th1 polarized cells, can express granzyme B and exert cytotoxic functions. Therefore, the expression of Granzyme B strengthens the argument for Th1 polarization of these activated CD4 T cells."]}},"pid":110158}
{"timestamp":"2025-06-25 17:55:41","session_id":"20250625_173119","level":"INFO","message":"Initialized gemini processor","context":{"provider":"gemini"},"pid":110158}
{"timestamp":"2025-06-25 17:55:41","session_id":"20250625_173119","level":"INFO","message":"Starting gemini API request","context":{"model":"gemini-1.5-pro","provider":"gemini"},"pid":110158} {"timestamp":"2025-06-25 17:55:41","session_id":"20250625_173119","level":"ERROR","message":"Gemini API request failed","context":{"error":"You exceeded your current quota, please check your plan and billing details. For more information on this error, head to: https://ai.google.dev/gemini-api/docs/rate-limits.","provider":"gemini","model":"gemini-1.5-pro","status_code":429},"pid":110158}
{"timestamp":"2025-06-25 17:55:41","session_id":"20250625_173119","level":"ERROR","message":"Failed to process chunk 1: Gemini API request failed: You exceeded your current quota, please check your plan and billing details. For more information on this error, head to: https://ai.google.dev/gemini-api/docs/rate-limits.","context":{"provider":"gemini","model":"gemini-1.5-pro","chunk":1,"error":"Gemini API request failed: You exceeded your current quota, please check your plan and billing details. For more information on this error, head to: https://ai.google.dev/gemini-api/docs/rate-limits."},"pid":110158} {"timestamp":"2025-06-25 17:55:41","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"gemini","chunks_processed":1},"pid":110158} {"timestamp":"2025-06-25 17:55:41","session_id":"20250625_173119","level":"ERROR","message":"No valid responses received","context":{"provider":"gemini","chunks_attempted":1},"pid":110158} {"timestamp":"2025-06-25 17:55:41","session_id":"20250625_173119","level":"INFO","message":"API call completed: gemini/gemini-1.5-pro (0.051s)","context":{"provider":"gemini","model":"gemini-1.5-pro","duration_seconds":0.051,"success":true,"tokens":{},"call_count":124},"pid":110158}
{"timestamp":"2025-06-25 17:55:41","session_id":"20250625_173119","level":"INFO","message":"API call completed: gemini/gemini-1.5-pro (0.053s)","context":{"provider":"gemini","model":"gemini-1.5-pro","duration_seconds":0.053,"success":true,"tokens":{},"call_count":125},"pid":110158}
{"timestamp":"2025-06-25 17:55:41","session_id":"20250625_173119","level":"INFO","message":"Model response received successfully","context":{"provider":"gemini","model":"gemini-1.5-pro","response_length":25,"duration_seconds":0.053},"pid":110158}
{"timestamp":"2025-06-25 17:55:41","session_id":"20250625_173119","level":"INFO","message":"Discussion prediction for cluster 12","context":{"cluster_id":"12","event_type":"prediction","data":{"model":"gemini-1.5-pro","round":1,"prediction":"Error: No valid responses"}},"pid":110158}
{"timestamp":"2025-06-25 17:55:41","session_id":"20250625_173119","level":"INFO","message":"Initialized grok processor","context":{"provider":"grok"},"pid":110158}
{"timestamp":"2025-06-25 17:55:41","session_id":"20250625_173119","level":"INFO","message":"Starting grok API request","context":{"model":"grok-3-latest","provider":"grok"},"pid":110158} {"timestamp":"2025-06-25 17:55:41","session_id":"20250625_173119","level":"ERROR","message":"Failed to process chunk 1: $ operator is invalid for atomic vectors","context":{"provider":"grok","model":"grok-3-latest","chunk":1,"error":"$ operator is invalid for atomic vectors"},"pid":110158} {"timestamp":"2025-06-25 17:55:41","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"grok","chunks_processed":1},"pid":110158} {"timestamp":"2025-06-25 17:55:41","session_id":"20250625_173119","level":"ERROR","message":"No valid responses received","context":{"provider":"grok","chunks_attempted":1},"pid":110158} {"timestamp":"2025-06-25 17:55:41","session_id":"20250625_173119","level":"INFO","message":"API call completed: grok/grok-3-latest (0.118s)","context":{"provider":"grok","model":"grok-3-latest","duration_seconds":0.118,"success":true,"tokens":{},"call_count":126},"pid":110158}
{"timestamp":"2025-06-25 17:55:41","session_id":"20250625_173119","level":"INFO","message":"API call completed: grok/grok-3-latest (0.120s)","context":{"provider":"grok","model":"grok-3-latest","duration_seconds":0.12,"success":true,"tokens":{},"call_count":127},"pid":110158}
{"timestamp":"2025-06-25 17:55:41","session_id":"20250625_173119","level":"INFO","message":"Model response received successfully","context":{"provider":"grok","model":"grok-3-latest","response_length":25,"duration_seconds":0.12},"pid":110158}
{"timestamp":"2025-06-25 17:55:41","session_id":"20250625_173119","level":"INFO","message":"Discussion prediction for cluster 12","context":{"cluster_id":"12","event_type":"prediction","data":{"model":"grok-3-latest","round":1,"prediction":"Error: No valid responses"}},"pid":110158}
{"timestamp":"2025-06-25 17:55:41","session_id":"20250625_173119","level":"INFO","message":"Initialized anthropic processor","context":{"provider":"anthropic"},"pid":110158}
{"timestamp":"2025-06-25 17:55:41","session_id":"20250625_173119","level":"INFO","message":"Starting anthropic API request","context":{"model":"claude-3-7-sonnet-20250219","provider":"anthropic"},"pid":110158} {"timestamp":"2025-06-25 17:55:41","session_id":"20250625_173119","level":"ERROR","message":"Anthropic API request failed","context":{"provider":"anthropic","model":"claude-3-7-sonnet-20250219","status_code":400,"error":"Your credit balance is too low to access the Anthropic API. Please go to Plans & Billing to upgrade or purchase credits."},"pid":110158}
{"timestamp":"2025-06-25 17:55:41","session_id":"20250625_173119","level":"ERROR","message":"Failed to process chunk 1: Anthropic API request failed: Your credit balance is too low to access the Anthropic API. Please go to Plans & Billing to upgrade or purchase credits.","context":{"provider":"anthropic","model":"claude-3-7-sonnet-20250219","chunk":1,"error":"Anthropic API request failed: Your credit balance is too low to access the Anthropic API. Please go to Plans & Billing to upgrade or purchase credits."},"pid":110158} {"timestamp":"2025-06-25 17:55:41","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"anthropic","chunks_processed":1},"pid":110158} {"timestamp":"2025-06-25 17:55:41","session_id":"20250625_173119","level":"ERROR","message":"No valid responses received","context":{"provider":"anthropic","chunks_attempted":1},"pid":110158} {"timestamp":"2025-06-25 17:55:41","session_id":"20250625_173119","level":"INFO","message":"API call completed: anthropic/claude-3-7-sonnet-20250219 (0.188s)","context":{"provider":"anthropic","model":"claude-3-7-sonnet-20250219","duration_seconds":0.188,"success":true,"tokens":{},"call_count":128},"pid":110158}
{"timestamp":"2025-06-25 17:55:41","session_id":"20250625_173119","level":"INFO","message":"API call completed: anthropic/claude-3-7-sonnet-20250219 (0.189s)","context":{"provider":"anthropic","model":"claude-3-7-sonnet-20250219","duration_seconds":0.189,"success":true,"tokens":{},"call_count":129},"pid":110158}
{"timestamp":"2025-06-25 17:55:41","session_id":"20250625_173119","level":"INFO","message":"Model response received successfully","context":{"provider":"anthropic","model":"claude-3-7-sonnet-20250219","response_length":25,"duration_seconds":0.189},"pid":110158}
{"timestamp":"2025-06-25 17:55:41","session_id":"20250625_173119","level":"INFO","message":"Discussion prediction for cluster 12","context":{"cluster_id":"12","event_type":"prediction","data":{"model":"claude-3-7-sonnet-20250219","round":1,"prediction":"Error: No valid responses"}},"pid":110158}
{"timestamp":"2025-06-25 17:55:41","session_id":"20250625_173119","level":"INFO","message":"Initialized openai processor","context":{"provider":"openai"},"pid":110158}
{"timestamp":"2025-06-25 17:55:41","session_id":"20250625_173119","level":"INFO","message":"Starting openai API request","context":{"model":"gpt-4o","provider":"openai"},"pid":110158} {"timestamp":"2025-06-25 17:55:42","session_id":"20250625_173119","level":"ERROR","message":"OpenAI API request failed","context":{"error":"You exceeded your current quota, please check your plan and billing details. For more information on this error, read the docs: https://platform.openai.com/docs/guides/error-codes/api-errors.","provider":"openai","model":"gpt-4o","status_code":429},"pid":110158}
{"timestamp":"2025-06-25 17:55:42","session_id":"20250625_173119","level":"ERROR","message":"Failed to process chunk 1: OpenAI API request failed: You exceeded your current quota, please check your plan and billing details. For more information on this error, read the docs: https://platform.openai.com/docs/guides/error-codes/api-errors.","context":{"provider":"openai","model":"gpt-4o","chunk":1,"error":"OpenAI API request failed: You exceeded your current quota, please check your plan and billing details. For more information on this error, read the docs: https://platform.openai.com/docs/guides/error-codes/api-errors."},"pid":110158} {"timestamp":"2025-06-25 17:55:42","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"openai","chunks_processed":1},"pid":110158} {"timestamp":"2025-06-25 17:55:42","session_id":"20250625_173119","level":"ERROR","message":"No valid responses received","context":{"provider":"openai","chunks_attempted":1},"pid":110158} {"timestamp":"2025-06-25 17:55:42","session_id":"20250625_173119","level":"INFO","message":"API call completed: openai/gpt-4o (0.166s)","context":{"provider":"openai","model":"gpt-4o","duration_seconds":0.166,"success":true,"tokens":{},"call_count":130},"pid":110158}
{"timestamp":"2025-06-25 17:55:42","session_id":"20250625_173119","level":"INFO","message":"API call completed: openai/gpt-4o (0.168s)","context":{"provider":"openai","model":"gpt-4o","duration_seconds":0.168,"success":true,"tokens":{},"call_count":131},"pid":110158}
{"timestamp":"2025-06-25 17:55:42","session_id":"20250625_173119","level":"INFO","message":"Model response received successfully","context":{"provider":"openai","model":"gpt-4o","response_length":25,"duration_seconds":0.168},"pid":110158}
{"timestamp":"2025-06-25 17:55:42","session_id":"20250625_173119","level":"INFO","message":"Discussion prediction for cluster 12","context":{"cluster_id":"12","event_type":"prediction","data":{"model":"gpt-4o","round":1,"prediction":"Error: No valid responses"}},"pid":110158}
{"timestamp":"2025-06-25 17:55:42","session_id":"20250625_173119","level":"WARN","message":"Model gemini-1.5-pro failed to provide valid response for cluster 12","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:55:42","session_id":"20250625_173119","level":"WARN","message":"Model grok-3-latest failed to provide valid response for cluster 12","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:55:42","session_id":"20250625_173119","level":"WARN","message":"Model claude-3-7-sonnet-20250219 failed to provide valid response for cluster 12","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:55:42","session_id":"20250625_173119","level":"WARN","message":"Model gpt-4o failed to provide valid response for cluster 12","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:55:42","session_id":"20250625_173119","level":"WARN","message":"Only 1 valid responses received for cluster 12. Skipping discussion.","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:55:42","session_id":"20250625_173119","level":"INFO","message":"Saved result to cache for cluster 12","context":{"cluster_id":"12"},"pid":110158}
{"timestamp":"2025-06-25 17:55:42","session_id":"20250625_173119","level":"INFO","message":"Completed discussion for cluster 12","context":{"cluster_id":"12"},"pid":110158} Completed discussion for cluster 12{"timestamp":"2025-06-25 17:55:42","session_id":"20250625_173119","level":"INFO","message":"Starting discussion for cluster 13...","context":{"cluster_id":"13"},"pid":110158}
Starting discussion for cluster 13...{"timestamp":"2025-06-25 17:55:42","session_id":"20250625_173119","level":"INFO","message":"Discussion start for cluster 13","context":{"cluster_id":"13","event_type":"start","data":{"tissue_name":"human blood CD4 T cells","marker_genes":"OASL,HERC5,IFIT3,IFIT2,ZBTB32,RHEBL1,NCF2,PLCG2,PMAIP1,IFIH1"}},"pid":110158}
{"timestamp":"2025-06-25 17:55:42","session_id":"20250625_173119","level":"INFO","message":"Initialized gemini processor","context":{"provider":"gemini"},"pid":110158}
{"timestamp":"2025-06-25 17:55:42","session_id":"20250625_173119","level":"INFO","message":"Starting gemini API request","context":{"model":"gemini-2.0-flash","provider":"gemini"},"pid":110158}
{"timestamp":"2025-06-25 17:55:48","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"gemini","chunks_processed":1},"pid":110158}
{"timestamp":"2025-06-25 17:55:48","session_id":"20250625_173119","level":"INFO","message":"Results consolidated successfully","context":{"provider":"gemini","valid_chunks":1,"total_lines":15},"pid":110158}
{"timestamp":"2025-06-25 17:55:48","session_id":"20250625_173119","level":"INFO","message":"API call completed: gemini/gemini-2.0-flash (6.122s)","context":{"provider":"gemini","model":"gemini-2.0-flash","duration_seconds":6.122,"success":true,"tokens":{},"call_count":132},"pid":110158}
{"timestamp":"2025-06-25 17:55:48","session_id":"20250625_173119","level":"INFO","message":"API call completed: gemini/gemini-2.0-flash (6.123s)","context":{"provider":"gemini","model":"gemini-2.0-flash","duration_seconds":6.123,"success":true,"tokens":{},"call_count":133},"pid":110158}
{"timestamp":"2025-06-25 17:55:48","session_id":"20250625_173119","level":"INFO","message":"Model response received successfully","context":{"provider":"gemini","model":"gemini-2.0-flash","response_length":[45,0,221,0,583,0,8,493,384,130,92,0,504,0,792],"duration_seconds":6.123},"pid":110158}
{"timestamp":"2025-06-25 17:55:48","session_id":"20250625_173119","level":"INFO","message":"Discussion prediction for cluster 13","context":{"cluster_id":"13","event_type":"prediction","data":{"model":"gemini-2.0-flash","round":1,"prediction":["CELL TYPE: Interferon-Stimulated CD4+ T cells","","GROUNDS: The cluster expresses the following genes: OASL, HERC5, IFIT3, IFIT2, IFIH1, ZBTB32, RHEBL1, NCF2, PLCG2, and PMAIP1. The presence of OASL, HERC5, IFIT3, IFIT2, and IFIH1 strongly suggests interferon stimulation.","","WARRANT: OASL, HERC5, IFIT3, IFIT2, and IFIH1 are well-established interferon-stimulated genes (ISGs). Their increased expression is a direct consequence of cellular exposure to interferons (primarily type I and II). The presence of these genes in conjunction with T cell origin (CD4+ T cells) implies that these CD4+ T cells have been exposed to and are responding to interferon signaling. Other genes like ZBTB32, NCF2, PLCG2 and PMAIP1 can have roles in immune modulation or activation, and although not as specific to ISGs, are consistent with an activated immune cell phenotype.","","BACKING:","* **Interferon-Stimulated Genes (ISGs):** Numerous studies have demonstrated the induction of OASL, HERC5, IFIT3, IFIT2, and IFIH1 by interferon signaling. A literature search on PubMed or Google Scholar using terms like \"Interferon-stimulated genes,\" \"ISG induction,\" \"OASL interferon,\" \"IFIT interferon,\" etc., will yield many relevant research articles. (e.g., Sadler, A. J., & Williams, B. R. (2008). Interferon-inducible antiviral effectors. *Nature Reviews Immunology, 8*(7), 559-568.)","* **T Cell Response to Interferons:** T cells are known to be responsive to both type I and type II interferons. Interferons can influence T cell activation, differentiation, and effector functions. (e.g., Schroder, K., Hertzog, P. J., Ravasi, T., & Hume, D. A. (2004). Interferon-γ: an overview of signals, mechanisms and functions. *Journal of Leukocyte Biology, 75*(2), 163-189.)","* **ZBTB32:** Research shows that ZBTB32 can function as a transcription factor in T cells and can influence T cell development.","* **NCF2, PLCG2, and PMAIP1** These genes are involved in immune cell activation pathways.","","QUALIFIER: The prediction is highly probable. The strong enrichment of multiple well-known ISGs makes interferon stimulation the most likely explanation. However, it is possible that the observed gene expression pattern could be influenced by other factors besides direct interferon exposure. Further experiments, such as measuring interferon levels in the surrounding environment or performing functional assays to assess the cells' response to interferons, would be needed to confirm this definitively.","","REBUTTAL: While other models failed to provide a specific prediction, gemini-2.0-flash predicted Interferon-stimulated T cells, which aligns with my prediction. The absence of a specific prediction from the other models does not necessarily negate this conclusion. Their algorithms may have different thresholds or rely on different datasets. The combination of multiple ISGs, alongside other immunologically relevant genes strongly suggests interferon stimulation. While other activation signals may influence gene expression, the ISG signature is the most prominent and biologically relevant signal in this data. The other genes listed (RHEBL1, NCF2, PLCG2, PMAIP1, ZBTB32) are consistent with an activated T cell state that could be secondary to or synergistic with interferon stimulation."]}},"pid":110158}
{"timestamp":"2025-06-25 17:55:48","session_id":"20250625_173119","level":"INFO","message":"Initialized gemini processor","context":{"provider":"gemini"},"pid":110158}
{"timestamp":"2025-06-25 17:55:48","session_id":"20250625_173119","level":"INFO","message":"Starting gemini API request","context":{"model":"gemini-1.5-pro","provider":"gemini"},"pid":110158} {"timestamp":"2025-06-25 17:55:48","session_id":"20250625_173119","level":"ERROR","message":"Gemini API request failed","context":{"error":"You exceeded your current quota, please check your plan and billing details. For more information on this error, head to: https://ai.google.dev/gemini-api/docs/rate-limits.","provider":"gemini","model":"gemini-1.5-pro","status_code":429},"pid":110158}
{"timestamp":"2025-06-25 17:55:48","session_id":"20250625_173119","level":"ERROR","message":"Failed to process chunk 1: Gemini API request failed: You exceeded your current quota, please check your plan and billing details. For more information on this error, head to: https://ai.google.dev/gemini-api/docs/rate-limits.","context":{"provider":"gemini","model":"gemini-1.5-pro","chunk":1,"error":"Gemini API request failed: You exceeded your current quota, please check your plan and billing details. For more information on this error, head to: https://ai.google.dev/gemini-api/docs/rate-limits."},"pid":110158} {"timestamp":"2025-06-25 17:55:48","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"gemini","chunks_processed":1},"pid":110158} {"timestamp":"2025-06-25 17:55:48","session_id":"20250625_173119","level":"ERROR","message":"No valid responses received","context":{"provider":"gemini","chunks_attempted":1},"pid":110158} {"timestamp":"2025-06-25 17:55:48","session_id":"20250625_173119","level":"INFO","message":"API call completed: gemini/gemini-1.5-pro (0.058s)","context":{"provider":"gemini","model":"gemini-1.5-pro","duration_seconds":0.058,"success":true,"tokens":{},"call_count":134},"pid":110158}
{"timestamp":"2025-06-25 17:55:48","session_id":"20250625_173119","level":"INFO","message":"API call completed: gemini/gemini-1.5-pro (0.060s)","context":{"provider":"gemini","model":"gemini-1.5-pro","duration_seconds":0.06,"success":true,"tokens":{},"call_count":135},"pid":110158}
{"timestamp":"2025-06-25 17:55:48","session_id":"20250625_173119","level":"INFO","message":"Model response received successfully","context":{"provider":"gemini","model":"gemini-1.5-pro","response_length":25,"duration_seconds":0.06},"pid":110158}
{"timestamp":"2025-06-25 17:55:48","session_id":"20250625_173119","level":"INFO","message":"Discussion prediction for cluster 13","context":{"cluster_id":"13","event_type":"prediction","data":{"model":"gemini-1.5-pro","round":1,"prediction":"Error: No valid responses"}},"pid":110158}
{"timestamp":"2025-06-25 17:55:48","session_id":"20250625_173119","level":"INFO","message":"Initialized grok processor","context":{"provider":"grok"},"pid":110158}
{"timestamp":"2025-06-25 17:55:48","session_id":"20250625_173119","level":"INFO","message":"Starting grok API request","context":{"model":"grok-3-latest","provider":"grok"},"pid":110158} {"timestamp":"2025-06-25 17:55:48","session_id":"20250625_173119","level":"ERROR","message":"Failed to process chunk 1: $ operator is invalid for atomic vectors","context":{"provider":"grok","model":"grok-3-latest","chunk":1,"error":"$ operator is invalid for atomic vectors"},"pid":110158} {"timestamp":"2025-06-25 17:55:48","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"grok","chunks_processed":1},"pid":110158} {"timestamp":"2025-06-25 17:55:48","session_id":"20250625_173119","level":"ERROR","message":"No valid responses received","context":{"provider":"grok","chunks_attempted":1},"pid":110158} {"timestamp":"2025-06-25 17:55:48","session_id":"20250625_173119","level":"INFO","message":"API call completed: grok/grok-3-latest (0.130s)","context":{"provider":"grok","model":"grok-3-latest","duration_seconds":0.13,"success":true,"tokens":{},"call_count":136},"pid":110158}
{"timestamp":"2025-06-25 17:55:48","session_id":"20250625_173119","level":"INFO","message":"API call completed: grok/grok-3-latest (0.131s)","context":{"provider":"grok","model":"grok-3-latest","duration_seconds":0.131,"success":true,"tokens":{},"call_count":137},"pid":110158}
{"timestamp":"2025-06-25 17:55:48","session_id":"20250625_173119","level":"INFO","message":"Model response received successfully","context":{"provider":"grok","model":"grok-3-latest","response_length":25,"duration_seconds":0.131},"pid":110158}
{"timestamp":"2025-06-25 17:55:48","session_id":"20250625_173119","level":"INFO","message":"Discussion prediction for cluster 13","context":{"cluster_id":"13","event_type":"prediction","data":{"model":"grok-3-latest","round":1,"prediction":"Error: No valid responses"}},"pid":110158}
{"timestamp":"2025-06-25 17:55:48","session_id":"20250625_173119","level":"INFO","message":"Initialized anthropic processor","context":{"provider":"anthropic"},"pid":110158}
{"timestamp":"2025-06-25 17:55:48","session_id":"20250625_173119","level":"INFO","message":"Starting anthropic API request","context":{"model":"claude-3-7-sonnet-20250219","provider":"anthropic"},"pid":110158} {"timestamp":"2025-06-25 17:55:48","session_id":"20250625_173119","level":"ERROR","message":"Anthropic API request failed","context":{"provider":"anthropic","model":"claude-3-7-sonnet-20250219","status_code":400,"error":"Your credit balance is too low to access the Anthropic API. Please go to Plans & Billing to upgrade or purchase credits."},"pid":110158}
{"timestamp":"2025-06-25 17:55:48","session_id":"20250625_173119","level":"ERROR","message":"Failed to process chunk 1: Anthropic API request failed: Your credit balance is too low to access the Anthropic API. Please go to Plans & Billing to upgrade or purchase credits.","context":{"provider":"anthropic","model":"claude-3-7-sonnet-20250219","chunk":1,"error":"Anthropic API request failed: Your credit balance is too low to access the Anthropic API. Please go to Plans & Billing to upgrade or purchase credits."},"pid":110158} {"timestamp":"2025-06-25 17:55:48","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"anthropic","chunks_processed":1},"pid":110158} {"timestamp":"2025-06-25 17:55:48","session_id":"20250625_173119","level":"ERROR","message":"No valid responses received","context":{"provider":"anthropic","chunks_attempted":1},"pid":110158} {"timestamp":"2025-06-25 17:55:48","session_id":"20250625_173119","level":"INFO","message":"API call completed: anthropic/claude-3-7-sonnet-20250219 (0.158s)","context":{"provider":"anthropic","model":"claude-3-7-sonnet-20250219","duration_seconds":0.158,"success":true,"tokens":{},"call_count":138},"pid":110158}
{"timestamp":"2025-06-25 17:55:48","session_id":"20250625_173119","level":"INFO","message":"API call completed: anthropic/claude-3-7-sonnet-20250219 (0.159s)","context":{"provider":"anthropic","model":"claude-3-7-sonnet-20250219","duration_seconds":0.159,"success":true,"tokens":{},"call_count":139},"pid":110158}
{"timestamp":"2025-06-25 17:55:48","session_id":"20250625_173119","level":"INFO","message":"Model response received successfully","context":{"provider":"anthropic","model":"claude-3-7-sonnet-20250219","response_length":25,"duration_seconds":0.159},"pid":110158}
{"timestamp":"2025-06-25 17:55:48","session_id":"20250625_173119","level":"INFO","message":"Discussion prediction for cluster 13","context":{"cluster_id":"13","event_type":"prediction","data":{"model":"claude-3-7-sonnet-20250219","round":1,"prediction":"Error: No valid responses"}},"pid":110158}
{"timestamp":"2025-06-25 17:55:48","session_id":"20250625_173119","level":"INFO","message":"Initialized openai processor","context":{"provider":"openai"},"pid":110158}
{"timestamp":"2025-06-25 17:55:48","session_id":"20250625_173119","level":"INFO","message":"Starting openai API request","context":{"model":"gpt-4o","provider":"openai"},"pid":110158} {"timestamp":"2025-06-25 17:55:48","session_id":"20250625_173119","level":"ERROR","message":"OpenAI API request failed","context":{"error":"You exceeded your current quota, please check your plan and billing details. For more information on this error, read the docs: https://platform.openai.com/docs/guides/error-codes/api-errors.","provider":"openai","model":"gpt-4o","status_code":429},"pid":110158}
{"timestamp":"2025-06-25 17:55:48","session_id":"20250625_173119","level":"ERROR","message":"Failed to process chunk 1: OpenAI API request failed: You exceeded your current quota, please check your plan and billing details. For more information on this error, read the docs: https://platform.openai.com/docs/guides/error-codes/api-errors.","context":{"provider":"openai","model":"gpt-4o","chunk":1,"error":"OpenAI API request failed: You exceeded your current quota, please check your plan and billing details. For more information on this error, read the docs: https://platform.openai.com/docs/guides/error-codes/api-errors."},"pid":110158} {"timestamp":"2025-06-25 17:55:48","session_id":"20250625_173119","level":"INFO","message":"All chunks processed, consolidating results","context":{"provider":"openai","chunks_processed":1},"pid":110158} {"timestamp":"2025-06-25 17:55:48","session_id":"20250625_173119","level":"ERROR","message":"No valid responses received","context":{"provider":"openai","chunks_attempted":1},"pid":110158} {"timestamp":"2025-06-25 17:55:48","session_id":"20250625_173119","level":"INFO","message":"API call completed: openai/gpt-4o (0.154s)","context":{"provider":"openai","model":"gpt-4o","duration_seconds":0.154,"success":true,"tokens":{},"call_count":140},"pid":110158}
{"timestamp":"2025-06-25 17:55:48","session_id":"20250625_173119","level":"INFO","message":"API call completed: openai/gpt-4o (0.155s)","context":{"provider":"openai","model":"gpt-4o","duration_seconds":0.155,"success":true,"tokens":{},"call_count":141},"pid":110158}
{"timestamp":"2025-06-25 17:55:48","session_id":"20250625_173119","level":"INFO","message":"Model response received successfully","context":{"provider":"openai","model":"gpt-4o","response_length":25,"duration_seconds":0.155},"pid":110158}
{"timestamp":"2025-06-25 17:55:48","session_id":"20250625_173119","level":"INFO","message":"Discussion prediction for cluster 13","context":{"cluster_id":"13","event_type":"prediction","data":{"model":"gpt-4o","round":1,"prediction":"Error: No valid responses"}},"pid":110158}
{"timestamp":"2025-06-25 17:55:48","session_id":"20250625_173119","level":"WARN","message":"Model gemini-1.5-pro failed to provide valid response for cluster 13","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:55:48","session_id":"20250625_173119","level":"WARN","message":"Model grok-3-latest failed to provide valid response for cluster 13","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:55:48","session_id":"20250625_173119","level":"WARN","message":"Model claude-3-7-sonnet-20250219 failed to provide valid response for cluster 13","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:55:48","session_id":"20250625_173119","level":"WARN","message":"Model gpt-4o failed to provide valid response for cluster 13","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:55:48","session_id":"20250625_173119","level":"WARN","message":"Only 1 valid responses received for cluster 13. Skipping discussion.","context":{},"pid":110158}
{"timestamp":"2025-06-25 17:55:48","session_id":"20250625_173119","level":"INFO","message":"Saved result to cache for cluster 13","context":{"cluster_id":"13"},"pid":110158}
{"timestamp":"2025-06-25 17:55:48","session_id":"20250625_173119","level":"INFO","message":"Completed discussion for cluster 13","context":{"cluster_id":"13"},"pid":110158} Completed discussion for cluster 13
Consensus Building Summary:
Total clusters analyzed: 1
Controversial clusters requiring discussion: 13
Detailed results for controversial clusters:
Cluster 1:
Initial predictions:
gemini-2.0-flash: 0: Proliferating T cells
gemini-1.5-pro: Error: No valid responses
grok-3-latest: Error: No valid responses
claude-3-7-sonnet-20250219: Error: No valid responses
gpt-4o: Error: No valid responses
Uncertainty metrics:
Consensus proportion: 0.00
Shannon entropy: 0.00
Final consensus: Not available
Cluster 2:
Initial predictions:
gemini-2.0-flash: 1: NK-like T cells
gemini-1.5-pro: No prediction provided
grok-3-latest: No prediction provided
claude-3-7-sonnet-20250219: No prediction provided
gpt-4o: No prediction provided
Uncertainty metrics:
Consensus proportion: 0.00
Shannon entropy: 0.00
Final consensus: Not available
Cluster 3:
Initial predictions:
gemini-2.0-flash: 2: Th2 cells
gemini-1.5-pro: No prediction provided
grok-3-latest: No prediction provided
claude-3-7-sonnet-20250219: No prediction provided
gpt-4o: No prediction provided
Uncertainty metrics:
Consensus proportion: 0.00
Shannon entropy: 0.00
Final consensus: Not available
Cluster 4:
Initial predictions:
gemini-2.0-flash: 3: Naive T cells (Male)
gemini-1.5-pro: No prediction provided
grok-3-latest: No prediction provided
claude-3-7-sonnet-20250219: No prediction provided
gpt-4o: No prediction provided
Uncertainty metrics:
Consensus proportion: 0.00
Shannon entropy: 0.00
Final consensus: Not available
Cluster 5:
Initial predictions:
gemini-2.0-flash: 4: Unknown
gemini-1.5-pro: No prediction provided
grok-3-latest: No prediction provided
claude-3-7-sonnet-20250219: No prediction provided
gpt-4o: No prediction provided
Uncertainty metrics:
Consensus proportion: 0.00
Shannon entropy: 0.00
Final consensus: Not available
Cluster 6:
Initial predictions:
gemini-2.0-flash: 5: Unknown
gemini-1.5-pro: No prediction provided
grok-3-latest: No prediction provided
claude-3-7-sonnet-20250219: No prediction provided
gpt-4o: No prediction provided
Uncertainty metrics:
Consensus proportion: 0.00
Shannon entropy: 0.00
Final consensus: Not available
Cluster 7:
Initial predictions:
gemini-2.0-flash: 6: Th2 cells
gemini-1.5-pro: No prediction provided
grok-3-latest: No prediction provided
claude-3-7-sonnet-20250219: No prediction provided
gpt-4o: No prediction provided
Uncertainty metrics:
Consensus proportion: 0.00
Shannon entropy: 0.00
Final consensus: Not available
Cluster 8:
Initial predictions:
gemini-2.0-flash: 7: T cells
gemini-1.5-pro: No prediction provided
grok-3-latest: No prediction provided
claude-3-7-sonnet-20250219: No prediction provided
gpt-4o: No prediction provided
Uncertainty metrics:
Consensus proportion: 0.00
Shannon entropy: 0.00
Final consensus: Not available
Cluster 9:
Initial predictions:
gemini-2.0-flash: 8: Unknown
gemini-1.5-pro: No prediction provided
grok-3-latest: No prediction provided
claude-3-7-sonnet-20250219: No prediction provided
gpt-4o: No prediction provided
Uncertainty metrics:
Consensus proportion: 0.00
Shannon entropy: 0.00
Final consensus: Not available
Cluster 10:
Initial predictions:
gemini-2.0-flash: 9: Cytotoxic T cells
gemini-1.5-pro: No prediction provided
grok-3-latest: No prediction provided
claude-3-7-sonnet-20250219: No prediction provided
gpt-4o: No prediction provided
Uncertainty metrics:
Consensus proportion: 0.00
Shannon entropy: 0.00
Final consensus: Not available
Cluster 11:
Initial predictions:
gemini-2.0-flash: 10: Naive T cells (Male)
gemini-1.5-pro: No prediction provided
grok-3-latest: No prediction provided
claude-3-7-sonnet-20250219: No prediction provided
gpt-4o: No prediction provided
Uncertainty metrics:
Consensus proportion: 0.00
Shannon entropy: 0.00
Final consensus: Not available
Cluster 12:
Initial predictions:
gemini-2.0-flash: 11: Activated T cells
gemini-1.5-pro: No prediction provided
grok-3-latest: No prediction provided
claude-3-7-sonnet-20250219: No prediction provided
gpt-4o: No prediction provided
Uncertainty metrics:
Consensus proportion: 0.00
Shannon entropy: 0.00
Final consensus: Not available
Cluster 13:
Initial predictions:
gemini-2.0-flash: 12: Activated T cells
gemini-1.5-pro: No prediction provided
grok-3-latest: No prediction provided
claude-3-7-sonnet-20250219: No prediction provided
gpt-4o: No prediction provided
Uncertainty metrics:
Consensus proportion: 0.00
Shannon entropy: 0.00
Final consensus: Not available# Add annotations to Seurat object
cluster_to_celltype_map <- consensus_results$final_annotations
# Create new cell type identifier column
cell_types <- as.character(Idents(pbmc))
for (cluster_id in names(cluster_to_celltype_map)) {
cell_types[cell_types == cluster_id] <- cluster_to_celltype_map[[cluster_id]]
}
# Add cell types to Seurat object
pbmc$mLLM_cell_type <- cell_types
# Visualize results
DimPlot(pbmc, group.by = "mLLM_cell_type", label = TRUE) +
ggtitle("mLLMCelltype Consensus Annotations")
4. Annotate with mLLM
# Load necessary packages
library(mLLMCelltype)
# Configure unified logging (optional - uses defaults if not specified)
configure_logger(level = "INFO", console_output = TRUE, json_format = TRUE)
# Create cache directory
cache_dir <- "./mllmcelltype_cache/"
dir.create(cache_dir, showWarnings = FALSE, recursive = TRUE)
# Read CSV file content
markers_file <- "cluster_genes_wide.csv"
file_content <- readLines(markers_file)
# Skip header row
data_lines <- file_content[-1]
# Convert data to list format, using numeric indices as keys
marker_genes_list <- list()
cluster_names <- c()
# First collect all cluster names
for(line in data_lines) {
parts <- strsplit(line, ",", fixed = TRUE)[[1]]
cluster_names <- c(cluster_names, parts[1])
}
# Then create marker_genes_list with numeric indices
for(i in 1:length(data_lines)) {
line <- data_lines[i]
parts <- strsplit(line, ",", fixed = TRUE)[[1]]
# First part is the cluster name
cluster_name <- parts[1]
# Use index as key (0-based index, compatible with Seurat)
cluster_id <- as.character(i - 1)
# Remaining parts are genes
genes <- parts[-1]
# Filter out NA and empty strings
genes <- genes[!is.na(genes) & genes != ""]
# Add to marker_genes_list
marker_genes_list[[cluster_id]] <- list(genes = genes)
}
api_keys <- list(
openai = Sys.getenv("OPENAI_API_KEY"),
gemini = Sys.getenv("GEMINI_API_KEY"),
grok = Sys.getenv("GROK_API_KEY"),
anthropic = Sys.getenv("ANTHROPIC_API_KEY"),
deepseek = Sys.getenv("DEEPSEEK_API_KEY")
)
# Run consensus annotation with paid models
consensus_results <- interactive_consensus_annotation(
input = marker_genes_list,
tissue_name = "human blood CD4 T cells",
models = c(
"gemini-2.0-flash",
"gemini-1.5-pro",
"qwen-max-2025-01-25",
"grok-3-latest",
"claude-3-7-sonnet-20250219",
"gpt-4o"
),
api_keys = api_keys,
controversy_threshold = 0.6,
entropy_threshold = 1.0,
max_discussion_rounds = 3,
cache_dir = cache_dir
)
# Alternatively, use free OpenRouter models (no credits required)
# Add OpenRouter API key to the api_keys list
api_keys$openrouter <- "your-openrouter-api-key"
# Run consensus annotation with free models
free_consensus_results <-
interactive_consensus_annotation(
input = marker_genes_list,
tissue_name = "your tissue type", # e.g., "human heart"
models = c(
"meta-llama/llama-4-maverick:free", # Meta Llama 4 Maverick (free)
"nvidia/llama-3.1-nemotron-ultra-253b-v1:free", # NVIDIA Nemotron Ultra 253B (free)
"deepseek/deepseek-chat-v3-0324:free", # DeepSeek Chat v3 (free)
"microsoft/mai-ds-r1:free" # Microsoft MAI-DS-R1 (free)
),
api_keys = api_keys,
consensus_check_model = "deepseek/deepseek-chat-v3-0324:free", # Free model for consensus checking
controversy_threshold = 0.6,
entropy_threshold = 1.0,
max_discussion_rounds = 2,
cache_dir = cache_dir
)
# Save results
saveRDS(consensus_results, "14_Clusters.rds")
# Print results summary
cat("\nResults summary:\n")
cat("Available fields:", paste(names(consensus_results), collapse=", "), "\n\n")
# Print final annotations
cat("Final cell type annotations:\n")
for(cluster in names(consensus_results$final_annotations)) {
cat(sprintf("%s: %s\n", cluster, consensus_results$final_annotations[[cluster]]))
}
5. Annotate with mLLM
# Load the package
library(mLLMCelltype)
library(SCpubr)
# Set API keys
Sys.setenv(ANTHROPIC_API_KEY = "your-anthropic-api-key")
Sys.setenv(OPENAI_API_KEY = "your-openai-api-key")
Sys.setenv(GEMINI_API_KEY = "your-gemini-api-key")
# Use multiple models for annotation
models <- c(
"claude-3-7-sonnet-20250219",
"gpt-4o",
"gemini-2.5-pro"
)
# Run multi-model annotation
results <- list()
for (model in models) {
provider <- get_provider(model)
api_key <- switch(provider,
"anthropic" = Sys.getenv("ANTHROPIC_API_KEY"),
"openai" = Sys.getenv("OPENAI_API_KEY"),
"gemini" = Sys.getenv("GEMINI_API_KEY"))
results[[model]] <- annotate_cell_types(
input = pbmc_markers,
tissue_name = "human PBMC",
model = model,
api_key = api_key
)
}
# Create consensus using interactive consensus annotation
api_keys <- list(
anthropic = Sys.getenv("ANTHROPIC_API_KEY"),
openai = Sys.getenv("OPENAI_API_KEY"),
gemini = Sys.getenv("GEMINI_API_KEY")
)
consensus_results <- interactive_consensus_annotation(
input = pbmc_markers,
tissue_name = "human PBMC",
models = models, # Use the models defined above
api_keys = api_keys,
controversy_threshold = 0.7,
entropy_threshold = 1.0,
max_discussion_rounds = 3,
consensus_check_model = "claude-3-7-sonnet-20250219"
)
# Print consensus results summary
print_consensus_summary(consensus_results)6. Annotate with mLLM
# Set OpenRouter API key
openrouter_api_key <- Sys.getenv("OPENROUTER_API_KEY")
# Define free OpenRouter models to use
free_models <- c(
"meta-llama/llama-4-maverick:free", # Meta Llama 4 Maverick (free)
"nvidia/llama-3.1-nemotron-ultra-253b-v1:free", # NVIDIA Nemotron Ultra 253B (free)
"deepseek/deepseek-chat-v3-0324:free", # DeepSeek Chat v3 (free)
"microsoft/mai-ds-r1:free" # Microsoft MAI-DS-R1 (free)
)
# Run annotation with free OpenRouter models
free_results <- list()
for (model in free_models) {
free_results[[model]] <- annotate_cell_types(
input = pbmc_markers,
tissue_name = "human PBMC",
model = model, # OpenRouter models are automatically detected by format: 'provider/model-name:free'
api_key = openrouter_api_key,
top_gene_count = 10
)
}
# Create consensus with free models
free_consensus_results <- interactive_consensus_annotation(
input = pbmc_markers,
tissue_name = "human PBMC",
models = free_models, # Use all the free models defined above
api_keys = list("openrouter" = openrouter_api_key),
controversy_threshold = 0.7,
entropy_threshold = 1.0,
consensus_check_model = "meta-llama/llama-4-maverick:free" # Use a free model for consensus checking
)
# View free model consensus results
# You can access the final annotations with free_consensus_results$final_annotations
# Add free model consensus annotations to Seurat object
pbmc$free_model_consensus <- plyr::mapvalues(
x = as.character(Idents(pbmc_small)),
from = as.character(0:(length(free_consensus_results$final_annotations)-1)),
to = free_consensus_results$final_annotations
)
# Compare paid vs. free model results
comparison <- data.frame(
cluster = as.character(0:(length(consensus_results$final_annotations)-1)),
paid_models = consensus_results$final_annotations,
free_models = free_consensus_results$final_annotations,
agreement = consensus_results$final_annotations == free_consensus_results$final_annotations
)
print(comparison)
---
title: "mLLM Annotatin of all clusters"
author: "Nasir Mahmood Abbasi"
date: "`r Sys.Date()`"
output:
  html_notebook:
    toc: yes
    toc_float: yes
    toc_collapsed: yes
  word_document:
    toc: yes
  html_document:
    toc: yes
    df_print: paged
  pdf_document:
    toc: yes
---


# 1. load libraries
```{r setup, include=FALSE}

library(Seurat)
library(monocle3)
library(ggplot2)
library(dplyr)
library(SCpubr)

# Load required libraries
library(Seurat)
library(Matrix)
library(data.table)
library(patchwork)


```


# 2. Load Seurat Object 
```{r}

All_samples_Merged <- readRDS("../0-Seurat_RDS_OBJECT_FINAL/All_samples_Merged_Harmony_integrated_HVG_Updated-17-6-2025-final.rds")


```




# 3. Annotate with mLLM
```{r}
pbmc <- All_samples_Merged

rm(All_samples_Merged)

gc()

library(mLLMCelltype)
library(Seurat)
library(dplyr)



# Assuming you already have a preprocessed Seurat object
# pbmc <- readRDS("your_seurat_object.rds")


DefaultAssay(pbmc) <- "SCT"

Idents(pbmc) <- "seurat_clusters"


# Find marker genes for each cluster
pbmc_markers <- FindAllMarkers(pbmc,
                           only.pos = TRUE,
                           min.pct = 0.25,
                           logfc.threshold = 0.25)

# Set up cache directory to speed up processing
cache_dir <- "./mllmcelltype_cache"
dir.create(cache_dir, showWarnings = FALSE, recursive = TRUE)



# Run LLMCelltype annotation with multiple LLM models
api_keys <- list(
  openai     = Sys.getenv("OPENAI_API_KEY"),
  gemini     = Sys.getenv("GEMINI_API_KEY"),
  grok       = Sys.getenv("GROK_API_KEY"),
  anthropic  = Sys.getenv("ANTHROPIC_API_KEY"),
  deepseek   = Sys.getenv("DEEPSEEK_API_KEY")
)


# Run consensus annotation with paid models
consensus_results <- interactive_consensus_annotation(
  input = pbmc_markers,
  tissue_name = "human blood CD4 T cells",
  models = c(
    "gemini-2.0-flash",
    "gemini-1.5-pro",
    "qwen-max-2025-01-25",
    "grok-3-latest",
    "claude-3-7-sonnet-20250219",
    "gpt-4o"
  ),
  api_keys = api_keys,
  controversy_threshold = 0.6,
  entropy_threshold = 1.0,
  max_discussion_rounds = 3,
  cache_dir = cache_dir
)

# Add annotations to Seurat object
cluster_to_celltype_map <- consensus_results$final_annotations

# Create new cell type identifier column
cell_types <- as.character(Idents(pbmc))
for (cluster_id in names(cluster_to_celltype_map)) {
  cell_types[cell_types == cluster_id] <- cluster_to_celltype_map[[cluster_id]]
}

# Add cell types to Seurat object
pbmc$mLLM_cell_type <- cell_types

# Visualize results
DimPlot(pbmc, group.by = "mLLM_cell_type", label = TRUE) +
  ggtitle("mLLMCelltype Consensus Annotations")
```


# 4. Annotate with mLLM
```{r}
# Load necessary packages
library(mLLMCelltype)

# Configure unified logging (optional - uses defaults if not specified)
configure_logger(level = "INFO", console_output = TRUE, json_format = TRUE)

# Create cache directory
cache_dir <- "./mllmcelltype_cache/"
dir.create(cache_dir, showWarnings = FALSE, recursive = TRUE)

# Read CSV file content
markers_file <- "cluster_genes_wide.csv"
file_content <- readLines(markers_file)

# Skip header row
data_lines <- file_content[-1]

# Convert data to list format, using numeric indices as keys
marker_genes_list <- list()
cluster_names <- c()

# First collect all cluster names
for(line in data_lines) {
  parts <- strsplit(line, ",", fixed = TRUE)[[1]]
  cluster_names <- c(cluster_names, parts[1])
}

# Then create marker_genes_list with numeric indices
for(i in 1:length(data_lines)) {
  line <- data_lines[i]
  parts <- strsplit(line, ",", fixed = TRUE)[[1]]

  # First part is the cluster name
  cluster_name <- parts[1]

  # Use index as key (0-based index, compatible with Seurat)
  cluster_id <- as.character(i - 1)

  # Remaining parts are genes
  genes <- parts[-1]

  # Filter out NA and empty strings
  genes <- genes[!is.na(genes) & genes != ""]

  # Add to marker_genes_list
  marker_genes_list[[cluster_id]] <- list(genes = genes)
}

api_keys <- list(
  openai     = Sys.getenv("OPENAI_API_KEY"),
  gemini     = Sys.getenv("GEMINI_API_KEY"),
  grok       = Sys.getenv("GROK_API_KEY"),
  anthropic  = Sys.getenv("ANTHROPIC_API_KEY"),
  deepseek   = Sys.getenv("DEEPSEEK_API_KEY")
)


# Run consensus annotation with paid models
consensus_results <- interactive_consensus_annotation(
  input = marker_genes_list,
  tissue_name = "human blood CD4 T cells",
  models = c(
    "gemini-2.0-flash",
    "gemini-1.5-pro",
    "qwen-max-2025-01-25",
    "grok-3-latest",
    "claude-3-7-sonnet-20250219",
    "gpt-4o"
  ),
  api_keys = api_keys,
  controversy_threshold = 0.6,
  entropy_threshold = 1.0,
  max_discussion_rounds = 3,
  cache_dir = cache_dir
)

# Alternatively, use free OpenRouter models (no credits required)
# Add OpenRouter API key to the api_keys list
api_keys$openrouter <- "your-openrouter-api-key"

# Run consensus annotation with free models
free_consensus_results <-
  interactive_consensus_annotation(
    input = marker_genes_list,
    tissue_name = "your tissue type", # e.g., "human heart"
    models = c(
      "meta-llama/llama-4-maverick:free",      # Meta Llama 4 Maverick (free)
      "nvidia/llama-3.1-nemotron-ultra-253b-v1:free",  # NVIDIA Nemotron Ultra 253B (free)
      "deepseek/deepseek-chat-v3-0324:free",   # DeepSeek Chat v3 (free)
      "microsoft/mai-ds-r1:free"               # Microsoft MAI-DS-R1 (free)
    ),
    api_keys = api_keys,
    consensus_check_model = "deepseek/deepseek-chat-v3-0324:free",  # Free model for consensus checking
    controversy_threshold = 0.6,
    entropy_threshold = 1.0,
    max_discussion_rounds = 2,
    cache_dir = cache_dir
  )

# Save results
saveRDS(consensus_results, "14_Clusters.rds")

# Print results summary
cat("\nResults summary:\n")
cat("Available fields:", paste(names(consensus_results), collapse=", "), "\n\n")

# Print final annotations
cat("Final cell type annotations:\n")
for(cluster in names(consensus_results$final_annotations)) {
  cat(sprintf("%s: %s\n", cluster, consensus_results$final_annotations[[cluster]]))
}

```


# 5. Annotate with mLLM
```{r}
# Load the package
library(mLLMCelltype)
library(SCpubr)

# Set API keys
Sys.setenv(ANTHROPIC_API_KEY = "your-anthropic-api-key")
Sys.setenv(OPENAI_API_KEY = "your-openai-api-key")
Sys.setenv(GEMINI_API_KEY = "your-gemini-api-key")

# Use multiple models for annotation
models <- c(
  "claude-3-7-sonnet-20250219",
  "gpt-4o",
  "gemini-2.5-pro"
)

# Run multi-model annotation
results <- list()
for (model in models) {
  provider <- get_provider(model)
  api_key <- switch(provider,
                   "anthropic" = Sys.getenv("ANTHROPIC_API_KEY"),
                   "openai" = Sys.getenv("OPENAI_API_KEY"),
                   "gemini" = Sys.getenv("GEMINI_API_KEY"))

  results[[model]] <- annotate_cell_types(
    input = pbmc_markers,
    tissue_name = "human PBMC",
    model = model,
    api_key = api_key
  )
}

# Create consensus using interactive consensus annotation
api_keys <- list(
  anthropic = Sys.getenv("ANTHROPIC_API_KEY"),
  openai = Sys.getenv("OPENAI_API_KEY"),
  gemini = Sys.getenv("GEMINI_API_KEY")
)

consensus_results <- interactive_consensus_annotation(
  input = pbmc_markers,
  tissue_name = "human PBMC",
  models = models,  # Use the models defined above
  api_keys = api_keys,
  controversy_threshold = 0.7,
  entropy_threshold = 1.0,
  max_discussion_rounds = 3,
  consensus_check_model = "claude-3-7-sonnet-20250219"
)

# Print consensus results summary
print_consensus_summary(consensus_results)
```


# 6. Annotate with mLLM
```{r}
# Set OpenRouter API key
openrouter_api_key <- Sys.getenv("OPENROUTER_API_KEY")

# Define free OpenRouter models to use
free_models <- c(
  "meta-llama/llama-4-maverick:free",                # Meta Llama 4 Maverick (free)
  "nvidia/llama-3.1-nemotron-ultra-253b-v1:free",    # NVIDIA Nemotron Ultra 253B (free)
  "deepseek/deepseek-chat-v3-0324:free",             # DeepSeek Chat v3 (free)
  "microsoft/mai-ds-r1:free"                         # Microsoft MAI-DS-R1 (free)
)

# Run annotation with free OpenRouter models
free_results <- list()
for (model in free_models) {
  free_results[[model]] <- annotate_cell_types(
    input = pbmc_markers,
    tissue_name = "human PBMC",
    model = model,  # OpenRouter models are automatically detected by format: 'provider/model-name:free'
    api_key = openrouter_api_key,
    top_gene_count = 10
  )
}

# Create consensus with free models
free_consensus_results <- interactive_consensus_annotation(
  input = pbmc_markers,
  tissue_name = "human PBMC",
  models = free_models,  # Use all the free models defined above
  api_keys = list("openrouter" = openrouter_api_key),
  controversy_threshold = 0.7,
  entropy_threshold = 1.0,
  consensus_check_model = "meta-llama/llama-4-maverick:free"  # Use a free model for consensus checking
)

# View free model consensus results
# You can access the final annotations with free_consensus_results$final_annotations

# Add free model consensus annotations to Seurat object
pbmc$free_model_consensus <- plyr::mapvalues(
  x = as.character(Idents(pbmc_small)),
  from = as.character(0:(length(free_consensus_results$final_annotations)-1)),
  to = free_consensus_results$final_annotations
)

# Compare paid vs. free model results
comparison <- data.frame(
  cluster = as.character(0:(length(consensus_results$final_annotations)-1)),
  paid_models = consensus_results$final_annotations,
  free_models = free_consensus_results$final_annotations,
  agreement = consensus_results$final_annotations == free_consensus_results$final_annotations
)
print(comparison)

```
