Codex GPT-5.5
replicate 1
passUDT-only
Answer
19159Workflow
Galaxy UDTCpG filtering and densitymethylation filtering
- Total tokens
- 886.8K
- Output
- 6.2K
New token-optimization experiment
Three additional GPT-5.6 Sol Galaxy replicates are available separately. Previous results remain unchanged.
Question
How many individual methylation measurements (rows) are removed when filtering out measurements that do not show >90% or <10% methylation in the Zebra Finch dataset?
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 2.22M total | 3/3 replicate 1 replicate 2 replicate 3 196.9K total |
| Codex GPT-5.6 Sol | 2/3 replicate 1 replicate 2 replicate 3 2.80M total | 3/3 replicate 1 replicate 2 replicate 3 190.4K total |
| Codex GPT-5.6 Luna | 1/3 replicate 1 replicate 2 replicate 3 13.90M total | 3/3 replicate 1 replicate 2 replicate 3 245.9K total |
| DeepSeek V4 Pro via Codex | 3/3 replicate 1 replicate 2 replicate 3 3.34M total | 3/3 replicate 1 replicate 2 replicate 3 267.8K total |
| DeepSeek V4 Pro via Claude Codesuperseded | 3/3 replicate 1 replicate 2 replicate 3 6.39M total | 2/3 replicate 1 replicate 2 replicate 3 4.37M total |
Execution condition
Galaxy-API code with skills
Codex GPT-5.5
3 primary replicatesCodex GPT-5.5
replicate 2
passUDT-only
Answer
19159Workflow
Galaxy UDTCpG filtering and densitymethylation filtering
- Total tokens
- 793.6K
- Output
- 6.0K
Codex GPT-5.5
replicate 3
pass
Answer
19159Workflow
Csv To TabularFilter rowsCpG filtering and densitymethylation filtering
- Total tokens
- 541.2K
- Output
- 5.4K
Codex GPT-5.6 Sol
3 primary replicatesCodex GPT-5.6 Sol
replicate 1
pass
Answer
19159Workflow
Csv To TabularFilter rowsWc GnuCpG filtering and densitymethylation filtering
- Total tokens
- 1.18M
- Output
- 5.2K
Codex GPT-5.6 Sol
replicate 2
pass
Answer
19159Workflow
Filter rowsWc GnuCpG filtering and densitymethylation filtering
- Total tokens
- 904.8K
- Output
- 5.2K
Codex GPT-5.6 Sol
replicate 3
fail
Why it missed
Header row was counted as dataThe Galaxy line count included the tabular header and returned 19,160. The number of removed methylation measurements is 19,159 data rows.
Answer
19160Workflow
Convert Characters1Filter rowsWc GnuCpG filtering and densitymethylation filtering
- Total tokens
- 712.1K
- Output
- 5.2K
Codex GPT-5.6 Luna
3 primary replicatesCodex GPT-5.6 Luna
replicate 1
pass
Answer
19159Workflow
Csv To TabularTable ComputeFilter Tabularmore stepsCpG filtering and densitymethylation filtering
- Total tokens
- 3.61M
- Output
- 22.2K
Codex GPT-5.6 Luna
replicate 2
fail
Why it missed
Header row was counted as dataThe Galaxy line count included the header and returned 19,160 instead of 19,159 removed measurements.
Answer
19160Workflow
Csv To TabularFilter rowsWc GnuCpG filtering and densitymethylation filtering
- Total tokens
- 1.62M
- Output
- 11.1K
Codex GPT-5.6 Luna
replicate 3
fail
Why it missed
Retained and removed rows were reversedGalaxy found 19,698 total rows and 19,159 rows in the inclusive 10-90% range. The agent subtracted those values and reported the complementary 539 retained extreme rows, but the question asks for the 19,159 removed rows.
Answer
539Workflow
Csv To TabularTable ComputeFilter TabularConvert Characters1Datamash summarymethylation filtering
- Total tokens
- 8.67M
- Output
- 28.4K
DeepSeek V4 Pro via Codex
3 primary replicatesDeepSeek V4 Pro via Codex
replicate 1
pass
Answer
19159Workflow
Filter rowsWc Gnumethylation filteringCpG filtering and density
- Total tokens
- 934.9K
- Output
- 8.3K
DeepSeek V4 Pro via Codex
replicate 2
pass
Answer
19159Workflow
Csv To TabularFilter rowsmethylation filtering
- Total tokens
- 1.43M
- Output
- 11.9K
DeepSeek V4 Pro via Codex
replicate 3
pass
Answer
19159Workflow
Csv To TabularFilter rowsWc Gnumethylation filteringmean summary
- Total tokens
- 975.5K
- Output
- 12.2K
DeepSeek V4 Pro via Claude CodeSuperseded
3 primary replicatesDeepSeek V4 Pro via Claude Code
replicate 1
passUDT + standard tools
Answer
19159Workflow
Csv To TabularTable ComputeFilter TabularGalaxy UDTmethylation filteringCpG filtering and density
- Total tokens
- 2.56M
- Output
- 32.0K
DeepSeek V4 Pro via Claude Code
replicate 2
pass
Answer
19159Workflow
Csv To TabularWc GnuFilter TabularTp Cut Toolmethylation filtering
- Total tokens
- 1.91M
- Output
- 20.9K
DeepSeek V4 Pro via Claude Code
replicate 3
pass
Answer
19159Workflow
Filter Tabularmethylation filteringCpG filtering and density
- Total tokens
- 1.92M
- Output
- 24.1K
Execution condition
Open-ended code with skills
Codex GPT-5.5
3 primary replicatesCodex GPT-5.5
replicate 1
pass
Answer
19159Workflow
Local analysisCpG filtering and densitymethylation filtering
- Total tokens
- 62.3K
- Output
- 1.2K
Codex GPT-5.5
replicate 2
pass
Answer
19159Workflow
Local analysisCpG filtering and densitymethylation filtering
- Total tokens
- 67.1K
- Output
- 1.1K
Codex GPT-5.5
replicate 3
pass
Answer
19159Workflow
Local analysisCpG filtering and densitymethylation filtering
- Total tokens
- 67.5K
- Output
- 1.1K
Codex GPT-5.6 Sol
3 primary replicatesCodex GPT-5.6 Sol
replicate 1
pass
Answer
19159Workflow
Local analysis
- Total tokens
- 58.2K
- Output
- 928
Codex GPT-5.6 Sol
replicate 2
pass
Answer
19159Workflow
Local analysis
- Total tokens
- 72.7K
- Output
- 908
Codex GPT-5.6 Sol
replicate 3
pass
Answer
19159Workflow
Local analysis
- Total tokens
- 59.5K
- Output
- 1.2K
Codex GPT-5.6 Luna
3 primary replicatesCodex GPT-5.6 Luna
replicate 1
pass
Answer
19159Workflow
Local analysis
- Total tokens
- 95.3K
- Output
- 1.5K
Codex GPT-5.6 Luna
replicate 2
pass
Answer
19159Workflow
Local analysis
- Total tokens
- 68.0K
- Output
- 1.5K
Codex GPT-5.6 Luna
replicate 3
pass
Answer
19159Workflow
Local analysis
- Total tokens
- 82.6K
- Output
- 1.7K
DeepSeek V4 Pro via Codex
3 primary replicatesDeepSeek V4 Pro via Codex
replicate 1
pass
Answer
19159Workflow
Local analysisCpG filtering and densitymethylation filtering
- Total tokens
- 81.2K
- Output
- 2.3K
DeepSeek V4 Pro via Codex
replicate 2
pass
Answer
19159Workflow
Local analysisCpG filtering and densitymethylation filtering
- Total tokens
- 74.6K
- Output
- 1.8K
DeepSeek V4 Pro via Codex
replicate 3
pass
Answer
19159Workflow
Local analysisCpG filtering and densitymethylation filtering
- Total tokens
- 111.9K
- Output
- 3.4K
DeepSeek V4 Pro via Claude CodeSuperseded
3 primary replicatesDeepSeek V4 Pro via Claude Code
replicate 1
pass
Answer
19159Workflow
Local analysisCpG filtering and densitymethylation filtering
- Total tokens
- 143.7K
- Output
- 1.3K
DeepSeek V4 Pro via Claude Code
replicate 2
pass
Answer
19159Workflow
Local analysisCpG filtering and densitymethylation filtering
- Total tokens
- 94.1K
- Output
- 833
DeepSeek V4 Pro via Claude Code
replicate 3
fail
Why it missed
Execution failureThis run exhausted 101 turns after repeated filename and file-location mistakes and never wrote an answer. The direct row count is 19,159.
Answer
not producedWorkflow
Local analysisCpG filtering and density
- Total tokens
- 4.13M
- Output
- 28.2K
bix-52-q7 · 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
19159- Total tokens
- 483.7K
- Input
- 479.7K
- Cached input
- 450.3K
- Output
- 4.0K
Galaxy-API code · October 2026
replicate 2
Correct
Answer
19159- Total tokens
- 615.7K
- Input
- 611.7K
- Cached input
- 584.7K
- Output
- 4.0K
Galaxy-API code · October 2026
replicate 3
Correct
Answer
19159- Total tokens
- 600.9K
- Input
- 595.8K
- Cached input
- 558.2K
- Output
- 5.0K
Open-ended code averaged 0.06M tokens; previous website Galaxy averaged 0.93M; the new Galaxy runs averaged 0.57M, or 8.93× 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.