Codex GPT-5.5
replicate 1
passUDT-only
Answer
1.1282568023118122e-07Workflow
Galaxy UDTCpG filtering and densitymethylation filtering
- Total tokens
- 610.3K
- Output
- 8.3K
New token-optimization experiment
Three additional GPT-5.6 Sol Galaxy replicates are available separately. Previous results remain unchanged.
Question
What is the mean of per-chromosome densities (CpGs per base pair) for filtered (>90% or <10% methylation) unique age-related CpGs across all chromosomes (only including those with at least one filtered CpG) in the Jackdaw genome?
Comparison
Pass counts and token totals across the same three replicates.
| Agent | Galaxy-API code | Open-ended code |
|---|---|---|
| Codex GPT-5.5 | 3/3 replicate 1 replicate 2 replicate 3 1.85M total | 3/3 replicate 1 replicate 2 replicate 3 304.2K total |
| Codex GPT-5.6 Sol | 3/3 replicate 1 replicate 2 replicate 3 9.14M total | 3/3 replicate 1 replicate 2 replicate 3 334.5K total |
| Codex GPT-5.6 Luna | 2/3 replicate 1 replicate 2 replicate 3 30.33M total | 3/3 replicate 1 replicate 2 replicate 3 601.2K total |
| DeepSeek V4 Pro via Codex | 3/3 replicate 1 replicate 2 replicate 3 9.49M total | 3/3 replicate 1 replicate 2 replicate 3 4.52M total |
| DeepSeek V4 Pro via Claude Codesuperseded | 3/3 replicate 1 replicate 2 replicate 3 12.89M total | 3/3 replicate 1 replicate 2 replicate 3 872.9K total |
Execution condition
Galaxy-API code with skills
Codex GPT-5.5
3 primary replicatesCodex GPT-5.5
replicate 2
passUDT-only
Answer
1.12825680231e-07Workflow
Galaxy UDTCpG filtering and densitymethylation filtering
- Total tokens
- 817.5K
- Output
- 8.3K
Codex GPT-5.5
replicate 3
passUDT-only
Answer
1.1282568023118122e-07Workflow
Galaxy UDTCpG filtering and densitymethylation filtering
- Total tokens
- 417.4K
- Output
- 5.5K
Codex GPT-5.6 Sol
3 primary replicatesCodex GPT-5.6 Sol
replicate 1
pass
Answer
1.12826e-07Workflow
Csv To TabularFilter TabularSelect columnsmore stepsSummary statisticsCpG filtering and density
- Total tokens
- 3.09M
- Output
- 10.6K
Codex GPT-5.6 Sol
replicate 2
pass
Answer
1.1282568023118e-07Workflow
Csv To TabularFilter rowsDatamash summarymore stepsAdd derived columnCpG filtering and density
- Total tokens
- 3.42M
- Output
- 12.8K
Codex GPT-5.6 Sol
replicate 3
pass
Answer
1.1282568023118e-07Workflow
Csv To TabularFilter rowsDatamash summarymore stepsAdd derived columnCpG filtering and density
- Total tokens
- 2.64M
- Output
- 10.5K
Codex GPT-5.6 Luna
3 primary replicatesCodex GPT-5.6 Luna
replicate 1
pass
Answer
1.1282568023118121808590038207938999097997615882758e-7Workflow
Csv To TabularFilter rowsDatamash summarymore stepsAdd derived columnCpG filtering and density
- Total tokens
- 9.72M
- Output
- 30.8K
Codex GPT-5.6 Luna
replicate 2
pass
Answer
1.1282568023118e-07Workflow
Csv To TabularFilter rowsSelect columnsmore stepsTp Sort Header ToolCpG filtering and density
- Total tokens
- 15.44M
- Output
- 41.5K
Codex GPT-5.6 Luna
replicate 3
fail
Why it missed
Filtering pipeline dropped qualifying chromosomesThis Galaxy branch retained filtered loci on only 18 chromosomes, while the verified strict-cutoff calculation has 51 unique CpGs across 20 chromosomes. Averaging the incomplete table produced 9.507e-08 instead of about 1.128e-07.
Answer
9.5074614121924e-08Workflow
Csv To TabularFilter TabularTp Grep Toolmore stepsTable ComputeCpG filtering and density
- Total tokens
- 5.17M
- Output
- 28.3K
DeepSeek V4 Pro via Codex
3 primary replicatesDeepSeek V4 Pro via Codex
replicate 1
pass
Answer
1.1282568023118e-07Workflow
Csv To TabularFilter rowsFilter Tabularmore stepsCpG filtering and densitymethylation filtering
- Total tokens
- 2.23M
- Output
- 20.4K
DeepSeek V4 Pro via Codex
replicate 2
pass
Answer
1.1282568023118119e-07Workflow
Filter rowsGroup and aggregateRemove headermore stepsCpG filtering and densitymethylation filtering
- Total tokens
- 3.91M
- Output
- 24.8K
DeepSeek V4 Pro via Codex
replicate 3
pass
Answer
1.1282568023118119e-07Workflow
Filter rowsGroup and aggregateSort rowsmore stepsmethylation filteringmean summary
- Total tokens
- 3.35M
- Output
- 28.3K
DeepSeek V4 Pro via Claude CodeSuperseded
3 primary replicatesDeepSeek V4 Pro via Claude Code
replicate 1
passUDT + standard tools
Answer
1.128256802311812e-07Workflow
Tp Head ToolGalaxy UDTGroup and aggregateCpG filtering and densitymethylation filtering
- Total tokens
- 3.67M
- Output
- 32.2K
DeepSeek V4 Pro via Claude Code
replicate 2
passUDT + standard tools
Answer
1.1282568023e-07Workflow
Filter TabularGalaxy UDTCpG filtering and densitymethylation filtering
- Total tokens
- 6.70M
- Output
- 60.1K
DeepSeek V4 Pro via Claude Code
replicate 3
pass
Answer
1.12826e-07Workflow
Filter rowsGroup and aggregateFilter Tabularmore stepsSummary statisticsCpG filtering and density
- Total tokens
- 2.52M
- Output
- 22.3K
Execution condition
Open-ended code with skills
Codex GPT-5.5
3 primary replicatesCodex GPT-5.5
replicate 1
pass
Answer
1.1282568023118122e-07Workflow
Local analysisCpG filtering and densitymethylation filtering
- Total tokens
- 83.0K
- Output
- 2.7K
Codex GPT-5.5
replicate 2
pass
Answer
1.1282568023118122e-07Workflow
Local analysisCpG filtering and densitymethylation filtering
- Total tokens
- 90.7K
- Output
- 2.3K
Codex GPT-5.5
replicate 3
pass
Answer
0.00000011282568023118121808590038207938999097997615882758Workflow
Local analysisCpG filtering and densitymethylation filtering
- Total tokens
- 130.5K
- Output
- 3.1K
Codex GPT-5.6 Sol
3 primary replicatesCodex GPT-5.6 Sol
replicate 1
pass
Answer
1.128256802311812e-7Workflow
Local analysis
- Total tokens
- 98.1K
- Output
- 2.2K
Codex GPT-5.6 Sol
replicate 2
pass
Answer
1.1282568023118122e-07Workflow
Local analysis
- Total tokens
- 140.1K
- Output
- 3.3K
Codex GPT-5.6 Sol
replicate 3
pass
Answer
1.1282568023118121808590038207938999098e-7Workflow
Local analysis
- Total tokens
- 96.4K
- Output
- 2.6K
Codex GPT-5.6 Luna
3 primary replicatesCodex GPT-5.6 Luna
replicate 1
pass
Answer
1.12825680231181218085900382079389990979976158827575984694831e-07Workflow
Local analysis
- Total tokens
- 275.6K
- Output
- 7.7K
Codex GPT-5.6 Luna
replicate 2
pass
Answer
1.1282568023118121808590038207938999097997615882758e-7Workflow
Local analysis
- Total tokens
- 149.2K
- Output
- 4.4K
Codex GPT-5.6 Luna
replicate 3
pass
Answer
1.1282568023118121808590038207938999e-7Workflow
Local analysis
- Total tokens
- 176.4K
- Output
- 6.3K
DeepSeek V4 Pro via Codex
3 primary replicatesDeepSeek V4 Pro via Codex
replicate 1
pass
Answer
1.1282568023118122e-07Workflow
Local analysisCpG filtering and densitymethylation filtering
- Total tokens
- 640.5K
- Output
- 10.9K
DeepSeek V4 Pro via Codex
replicate 2
pass
Answer
1.1282568023118122e-07Workflow
Local analysisCpG filtering and densitymethylation filteringmean summarymedian summary
- Total tokens
- 2.16M
- Output
- 24.5K
DeepSeek V4 Pro via Codex
replicate 3
pass
Answer
1.1282568023118122e-07Workflow
Local analysisCpG filtering and densitymethylation filteringmean summarymedian summary
- Total tokens
- 1.73M
- Output
- 23.3K
DeepSeek V4 Pro via Claude CodeSuperseded
3 primary replicatesDeepSeek V4 Pro via Claude Code
replicate 1
pass
Answer
1.1282568023118119e-07Workflow
Local analysisCpG filtering and densitymethylation filtering
- Total tokens
- 213.8K
- Output
- 3.9K
DeepSeek V4 Pro via Claude Code
replicate 2
pass
Answer
1.128256802311812e-07Workflow
Local analysisCpG filtering and densitymethylation filtering
- Total tokens
- 423.0K
- Output
- 7.1K
DeepSeek V4 Pro via Claude Code
replicate 3
pass
Answer
1.128256802311812e-07Workflow
Local analysisCpG filtering and densitymethylation filtering
- Total tokens
- 236.2K
- Output
- 4.0K
bix-52-q2 · October 2026 · three additional replicates
GPT-5.6 Sol · token optimization
Galaxy-API code, high reasoning, Fast service. Previous runs are retained above.
Galaxy-API code · October 2026
replicate 1
Correct
Answer
1.1282568023118e-07- Total tokens
- 1.19M
- Input
- 1.19M
- Cached input
- 1.13M
- Output
- 6.0K
Galaxy-API code · October 2026
replicate 2
Correct
Answer
1.1282568023118121875e-7- Total tokens
- 2.45M
- Input
- 2.44M
- Cached input
- 2.37M
- Output
- 9.2K
Galaxy-API code · October 2026
replicate 3
Correct
Answer
1.1282568023118e-07- Total tokens
- 1.51M
- Input
- 1.51M
- Cached input
- 1.44M
- Output
- 5.9K
Open-ended code averaged 0.11M tokens; previous website Galaxy averaged 3.05M; the new Galaxy runs averaged 1.72M, or 15.41× Open-ended code. Each mean covers three replicates of this same task with GPT-5.6 Sol.
Cached input is already included in input tokens. Full nested tool/job evidence is in each HF run's galaxy_execution_records.tar.gz, with an accompanying member index.