BixBench current item

bix-26-q5

Question

In P. aeruginosa KEGG pathway enrichment analysis, how many pathways are significantly enriched under iron-depleted conditions but show no significant enrichment under innate media conditions? Perform KEGG pathway enrichment analysis using genes with |log2FoldChange| > 1.5 and adjusted p-value < 0.05. Consider pathways significantly enriched if their enrichment adjusted p-value < 0.05.

Accepted answer
3
Domain
transcriptomics

Comparison

Pass counts and token totals across the same three replicates.

AgentGalaxy-API codeOpen-ended code
Codex GPT-5.50/3
replicate 1 replicate 2 replicate 3
5.01M total		0/3
replicate 1 replicate 2 replicate 3
1.77M total
Codex GPT-5.6 Sol0/3
replicate 1 replicate 2 replicate 3
5.30M total		0/3
replicate 1 replicate 2 replicate 3
1.28M total
Codex GPT-5.6 Luna0/3
replicate 1 replicate 2 replicate 3
52.59M total		0/3
replicate 1 replicate 2 replicate 3
4.86M total
DeepSeek V4 Pro via Codex0/3
replicate 1 replicate 2 replicate 3
16.21M total		0/3
replicate 1 replicate 2 replicate 3
13.08M total
DeepSeek V4 Pro via Claude Codesuperseded0/3
replicate 1 replicate 2 replicate 3
7.54M total		1/3
replicate 1 replicate 2 replicate 3
4.62M total

Execution condition

Galaxy-API code with skills

Codex GPT-5.5

3 primary replicates
Codex GPT-5.5

replicate 1

failUDT + standard tools

Why it missed

Scientific route errorThis run combined up- and down-regulated genes into one foreground per condition. The reference analysis tests each direction separately before comparing pathway sets, which gives three iron-only pathways rather than two.
Answer2
Workflow
Rds To TabularGalaxy UDTKegg Ora
Total tokens
1.64M
Output
10.7K
Galaxy historyRun trace
Codex GPT-5.5

replicate 2

failUDT + standard tools

Why it missed

Scientific route errorThis run combined up- and down-regulated genes into one foreground per condition. The reference analysis tests each direction separately before comparing pathway sets, which gives three iron-only pathways rather than two.
Answer2
Workflow
Rds To TabularGalaxy UDTKegg Ora
Total tokens
1.51M
Output
10.8K
Galaxy historyRun trace
Codex GPT-5.5

replicate 3

failUDT + standard tools

Why it missed

Scientific route errorThis run combined up- and down-regulated genes into one foreground per condition. The reference analysis tests each direction separately before comparing pathway sets, which gives three iron-only pathways rather than two.
Answer2
Workflow
Rds To TabularGalaxy UDTKegg Ora
Total tokens
1.85M
Output
12.6K
Galaxy historyRun trace

Codex GPT-5.6 Sol

3 primary replicates
Codex GPT-5.6 Sol

replicate 1

fail

Why it missed

Regulation directions were mergedThis run combined up- and down-regulated genes into one enrichment foreground per condition. The reference analysis tests the two directions separately before comparing pathway sets and finds three, not two, iron-only pathways.
Answer2
Workflow
Rds To TabularFilter rowsKegg Ora
Total tokens
2.32M
Output
10.9K
Galaxy historyRun trace
Codex GPT-5.6 Sol

replicate 2

fail

Why it missed

Regulation directions were mergedThis run combined up- and down-regulated genes into one enrichment foreground per condition. The reference analysis tests the two directions separately before comparing pathway sets and finds three, not two, iron-only pathways.
Answer2
Workflow
Rds To TabularFilter rowsKegg Ora
Total tokens
1.65M
Output
8.4K
Galaxy historyRun trace
Codex GPT-5.6 Sol

replicate 3

fail

Why it missed

Regulation directions were mergedThis run combined up- and down-regulated genes into one enrichment foreground per condition. The reference analysis tests the two directions separately before comparing pathway sets and finds three, not two, iron-only pathways.
Answer2
Workflow
Rds To TabularFilter rowsKegg Ora
Total tokens
1.33M
Output
7.1K
Galaxy historyRun trace

Codex GPT-5.6 Luna

3 primary replicates
Codex GPT-5.6 Luna

replicate 1

fail

Why it missed

Regulation directions were mergedThis run used one enrichment foreground per condition instead of separate up- and down-regulated branches. That changed the tests and consistently returned two rather than three iron-only pathways.
Answer2
Workflow
Rds To TabularFilter rowsSelect columnsKegg OraRegexcolumn1Tp Find And Replace
Total tokens
10.06M
Output
36.8K
Galaxy historyRun trace
Codex GPT-5.6 Luna

replicate 2

fail

Why it missed

Regulation directions were mergedThis run used one enrichment foreground per condition instead of separate up- and down-regulated branches. That changed the tests and consistently returned two rather than three iron-only pathways.
Answer2
Workflow
Rds To TabularFilter rowsFilter TabularSelect columnsKegg Ora
Total tokens
4.93M
Output
21.6K
Galaxy historyRun trace
Codex GPT-5.6 Luna

replicate 3

failUDT + standard tools

Why it missed

Regulation directions were mergedThis run used one enrichment foreground per condition instead of separate up- and down-regulated branches. That changed the tests and consistently returned two rather than three iron-only pathways.
Answer2
Workflow
Rds To TabularFilter rowsSelect columnsmore stepsUpload datasetSciPy
Total tokens
37.60M
Output
67.4K
Galaxy historyRun trace

DeepSeek V4 Pro via Codex

3 primary replicates
DeepSeek V4 Pro via Codex

replicate 1

fail

Evaluation status

Manual review pendingThe evaluator marked this answer incorrect. The answer, workflow summary, usage, and available run records are linked, but a manual root-cause audit has not yet been added.
Answer1
Workflow
Rds To TabularShow Beginning1Filter rowsSelect columnsKegg Ora
Total tokens
6.25M
Output
31.8K
Galaxy historyRun trace
DeepSeek V4 Pro via Codex

replicate 2

fail

Evaluation status

Manual review pendingThe evaluator marked this answer incorrect. The answer, workflow summary, usage, and available run records are linked, but a manual root-cause audit has not yet been added.
Answer2
Workflow
Galaxy via BioBlendDESeq2KEGGclusterProfiler
Total tokens
8.80M
Output
39.6K
Galaxy historyRun trace
DeepSeek V4 Pro via Codex

replicate 3

fail

Evaluation status

Manual review pendingThe evaluator marked this answer incorrect. The answer, workflow summary, usage, and available run records are linked, but a manual root-cause audit has not yet been added.
Answer1
Workflow
Rds To TabularKegg Ora
Total tokens
1.17M
Output
16.0K
Galaxy historyRun trace

DeepSeek V4 Pro via Claude CodeSuperseded

3 primary replicates
DeepSeek V4 Pro via Claude Code

replicate 1

failUDT + standard tools

Why it missed

Scientific route errorThis run used one ORA foreground per condition instead of separate up- and down-regulated branches. That changed the enrichment tests and returned two rather than the reference count of three.
Answer2
Workflow
Rds To TabularGalaxy UDTKegg OraDESeq2
Total tokens
3.24M
Output
37.1K
Galaxy historyRun trace
DeepSeek V4 Pro via Claude Code

replicate 2

fail

Why it missed

Scientific route errorThis run used one ORA foreground per condition instead of separate up- and down-regulated branches. That changed the enrichment tests and returned two rather than the reference count of three.
Answer2
Workflow
Rds To TabularFilter rowsSelect columnsKegg Ora
Total tokens
2.09M
Output
15.7K
Galaxy historyRun trace
DeepSeek V4 Pro via Claude Code

replicate 3

fail

Why it missed

Scientific route errorThis run used one ORA foreground per condition instead of separate up- and down-regulated branches. That changed the enrichment tests and returned two rather than the reference count of three.
Answer2
Workflow
Rds To TabularKegg Orafold-change calculation
Total tokens
2.21M
Output
19.4K
Galaxy historyRun trace

Execution condition

Open-ended code with skills

Codex GPT-5.5

3 primary replicates
Codex GPT-5.5

replicate 1

fail

Why it missed

Scientific route errorThis run pooled up- and down-regulated genes during ORA and returned two. Keeping regulation direction separate throughout enrichment gives three iron-only pathways.
Answer2
Workflow
Local analysisSciPystatsmodels
Total tokens
522.0K
Output
8.2K
Run trace
Codex GPT-5.5

replicate 2

fail

Why it missed

Incomplete condition comparisonThis run did not carry both regulation directions through the complete comparison of iron-depleted and innate-media pathway sets, so it counted only one iron-only pathway instead of three.
Answer1
Workflow
Local analysisclusterProfiler
Total tokens
556.0K
Output
6.7K
Run trace
Codex GPT-5.5

replicate 3

fail

Why it missed

Scientific route errorThis run pooled up- and down-regulated genes during ORA and returned two. Keeping regulation direction separate throughout enrichment gives three iron-only pathways.
Answer2
Workflow
Local analysisKEGGclusterProfiler
Total tokens
693.7K
Output
8.8K
Run trace

Codex GPT-5.6 Sol

3 primary replicates
Codex GPT-5.6 Sol

replicate 1

fail

Why it missed

Incomplete directional ORA comparisonThis run did not preserve and compare all separate up- and down-regulated enrichment branches for both conditions, so it counted one iron-only pathway instead of the reference three.
Answer1
Workflow
Local analysis
Total tokens
227.8K
Output
5.7K
Run trace
Codex GPT-5.6 Sol

replicate 2

fail

Why it missed

Incomplete directional ORA comparisonThis run did not preserve and compare all separate up- and down-regulated enrichment branches for both conditions, so it counted one iron-only pathway instead of the reference three.
Answer1
Workflow
Local analysis
Total tokens
723.1K
Output
9.1K
Run trace
Codex GPT-5.6 Sol

replicate 3

fail

Why it missed

Incomplete directional ORA comparisonThis run did not preserve and compare all separate up- and down-regulated enrichment branches for both conditions, so it counted one iron-only pathway instead of the reference three.
Answer1
Workflow
Local analysis
Total tokens
332.8K
Output
6.4K
Run trace

Codex GPT-5.6 Luna

3 primary replicates
Codex GPT-5.6 Luna

replicate 1

fail

Why it missed

Incomplete directional ORA comparisonThis run did not carry the separate regulation directions through the complete comparison of both conditions, so it counted one iron-only pathway instead of the reference three.
Answer1
Workflow
Local analysis
Total tokens
1.72M
Output
20.1K
Run trace
Codex GPT-5.6 Luna

replicate 2

fail

Why it missed

Incomplete directional ORA comparisonThis run did not carry the separate regulation directions through the complete comparison of both conditions, so it counted one iron-only pathway instead of the reference three.
Answer1
Workflow
Local analysis
Total tokens
1.56M
Output
15.3K
Run trace
Codex GPT-5.6 Luna

replicate 3

fail

Why it missed

Incomplete directional ORA comparisonThis run did not carry the separate regulation directions through the complete comparison of both conditions, so it counted one iron-only pathway instead of the reference three.
Answer1
Workflow
Local analysis
Total tokens
1.58M
Output
18.5K
Run trace

DeepSeek V4 Pro via Codex

3 primary replicates
DeepSeek V4 Pro via Codex

replicate 1

fail

Evaluation status

Manual review pendingThe evaluator marked this answer incorrect. The answer, workflow summary, usage, and available run records are linked, but a manual root-cause audit has not yet been added.
Answer1
Workflow
Local analysisclusterProfilerSciPystatsmodelsGSEApyKEGG
Total tokens
6.15M
Output
36.8K
Run trace
DeepSeek V4 Pro via Codex

replicate 2

fail

Evaluation status

Manual review pendingThe evaluator marked this answer incorrect. The answer, workflow summary, usage, and available run records are linked, but a manual root-cause audit has not yet been added.
Answer1
Workflow
Local analysisDESeq2clusterProfilerKEGGSciPystatsmodels
Total tokens
4.03M
Output
26.9K
Run trace
DeepSeek V4 Pro via Codex

replicate 3

fail

Evaluation status

Manual review pendingThe evaluator marked this answer incorrect. The answer, workflow summary, usage, and available run records are linked, but a manual root-cause audit has not yet been added.
Answer1
Workflow
Local analysisDESeq2clusterProfilerKEGG
Total tokens
2.91M
Output
23.2K
Run trace

DeepSeek V4 Pro via Claude CodeSuperseded

3 primary replicates
DeepSeek V4 Pro via Claude Code

replicate 1

fail

Why it missed

Scientific route errorThis run merged up- and down-regulated genes into one enrichment foreground. The reference analysis tests the two directions separately and finds three iron-only pathways rather than two.
Answer2
Workflow
Local analysisDESeq2clusterProfilerGSEApyBiopythonSciPy
Total tokens
2.28M
Output
39.6K
Run trace
DeepSeek V4 Pro via Claude Code

replicate 2

fail

Why it missed

Scientific route errorThis run merged up- and down-regulated genes into one enrichment foreground. The reference analysis tests the two directions separately and finds three iron-only pathways rather than two.
Answer2
Workflow
Local analysisDESeq2SciPystatsmodelsFisher exact test
Total tokens
1.48M
Output
13.4K
Run trace
DeepSeek V4 Pro via Claude Code

replicate 3

pass
Answer3
Workflow
Local analysisDESeq2GSEApyfold-change calculationBiopythonKEGG
Total tokens
866.6K
Output
14.0K
Run trace

bix-26-q5 · October 2026 · three additional replicates

GPT-5.6 Sol · token optimization

Galaxy-API code, high reasoning, Fast service. Previous runs are retained above.

Open-ended code averaged 0.43M tokens; previous website Galaxy averaged 1.77M; the new Galaxy runs averaged 0.77M, or 1.80× 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.

Optimization overview and all 150 runs