BixBench current item

bix-61-q5

Question

What is the Ts/Tv ratio for the MDR sample (SRR35233585) rounded to 2 decimal places?

Accepted answer
2.68
Domain
variant callset

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
1.46M total		0/3
replicate 1 replicate 2 replicate 3
473.2K total
Codex GPT-5.6 Sol0/3
replicate 1 replicate 2 replicate 3
1.53M total		0/3
replicate 1 replicate 2 replicate 3
772.3K total
Codex GPT-5.6 Luna0/3
replicate 1 replicate 2 replicate 3
3.87M total		0/3
replicate 1 replicate 2 replicate 3
1.31M total
DeepSeek V4 Pro via Codex0/3
replicate 1 replicate 2 replicate 3
5.66M total		0/3
replicate 1 replicate 2 replicate 3
2.42M total
DeepSeek V4 Pro via Claude Codesuperseded0/3
replicate 1 replicate 2 replicate 3 · invalid
1.53M total		0/3
replicate 1 replicate 2 replicate 3
1.49M total

Execution condition

Galaxy-API code with skills

Codex GPT-5.5

3 primary replicates
Codex GPT-5.5

replicate 1

fail

Why it missed

Benchmark provenance issueThis run used bcftools on the supplied raw VCF and obtained 2.56. The gold 2.68 appears to come from a different filtered or regenerated callset whose provenance is not included with the item.
Answer2.56
Workflow
Bcftools Stats
Total tokens
403.5K
Output
4.5K
Galaxy historyRun trace
Codex GPT-5.5

replicate 2

fail

Why it missed

Benchmark provenance issueThis run used bcftools on the supplied raw VCF and obtained 2.56. The gold 2.68 appears to come from a different filtered or regenerated callset whose provenance is not included with the item.
Answer2.56
Workflow
Bcftools Stats
Total tokens
555.5K
Output
5.3K
Galaxy historyRun trace
Codex GPT-5.5

replicate 3

fail

Why it missed

Benchmark provenance issueThis run used bcftools on the supplied raw VCF and obtained 2.56. The gold 2.68 appears to come from a different filtered or regenerated callset whose provenance is not included with the item.
Answer2.56
Workflow
Bcftools Stats
Total tokens
503.0K
Output
3.6K
Galaxy historyRun trace

Codex GPT-5.6 Sol

3 primary replicates
Codex GPT-5.6 Sol

replicate 1

fail

Why it missed

Benchmark provenance issueThis run computed 2.56 from the supplied raw VCF. The accepted 2.68 appears to come from a different filtered or regenerated callset that the item does not reproducibly identify.
Answer2.56
Workflow
Bcftools Stats
Total tokens
467.8K
Output
4.1K
Galaxy historyRun trace
Codex GPT-5.6 Sol

replicate 2

fail

Why it missed

Benchmark provenance issueThis run computed 2.56 from the supplied raw VCF. The accepted 2.68 appears to come from a different filtered or regenerated callset that the item does not reproducibly identify.
Answer2.56
Workflow
Bcftools Stats
Total tokens
486.7K
Output
3.8K
Galaxy historyRun trace
Codex GPT-5.6 Sol

replicate 3

fail

Why it missed

Benchmark provenance issueThis run computed 2.56 from the supplied raw VCF. The accepted 2.68 appears to come from a different filtered or regenerated callset that the item does not reproducibly identify.
Answer2.56
Workflow
Bcftools Stats
Total tokens
578.5K
Output
3.1K
Galaxy historyRun trace

Codex GPT-5.6 Luna

3 primary replicates
Codex GPT-5.6 Luna

replicate 1

fail

Why it missed

Benchmark provenance issueThis run computed 2.56 from the supplied raw VCF. The accepted 2.68 appears to depend on a different callset that is not included or reproducibly specified.
Answer2.56
Workflow
Bcftools Stats
Total tokens
1.40M
Output
11.0K
Galaxy historyRun trace
Codex GPT-5.6 Luna

replicate 2

fail

Why it missed

Benchmark provenance issueThis run computed 2.56 from the supplied raw VCF. The accepted 2.68 appears to depend on a different callset that is not included or reproducibly specified.
Answer2.56
Workflow
Bcftools Stats
Total tokens
1.08M
Output
14.5K
Galaxy historyRun trace
Codex GPT-5.6 Luna

replicate 3

fail

Why it missed

Benchmark provenance issueThis run computed 2.56 from the supplied raw VCF. The accepted 2.68 appears to depend on a different callset that is not included or reproducibly specified.
Answer2.56
Workflow
Bcftools Stats
Total tokens
1.39M
Output
9.3K
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.
Answer2.56
Workflow
Galaxy via BioBlendbcftools
Total tokens
2.28M
Output
13.2K
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.
Answer2.56
Workflow
Galaxy historypysambcftoolsVCFtools
Total tokens
1.13M
Output
12.0K
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.
Answer2.56
Workflow
Galaxy via BioBlendpysambcftoolsVCFtools
Total tokens
2.25M
Output
18.6K
Galaxy historyRun trace

DeepSeek V4 Pro via Claude CodeSuperseded

3 primary replicates
DeepSeek V4 Pro via Claude Code

replicate 1

fail

Why it missed

Benchmark provenance issueThis run computed 2.56 from the supplied raw VCF. The accepted 2.68 value depends on a different callset that the item does not reproducibly identify.
Answer2.56
Workflow
Bcftools Stats
Total tokens
546.2K
Output
6.5K
Galaxy historyRun trace
DeepSeek V4 Pro via Claude Code

replicate 2

fail

Why it missed

Benchmark provenance issueThis run computed 2.56 from the supplied raw VCF. The accepted 2.68 value depends on a different callset that the item does not reproducibly identify.
Answer2.56
Workflow
Bcftools Stats
Total tokens
457.5K
Output
4.2K
Galaxy historyRun trace
DeepSeek V4 Pro via Claude Code

replicate 3

invalid

Why this run is invalid

Invalid cross-replicate reuseThis run did not independently execute the analysis. It downloaded and used replicate 1's completed bcftools output, so the run is invalid.
Answer2.56
Workflow
Galaxy via BioBlendbcftools
Total tokens
522.9K
Output
3.6K
Galaxy historyRun trace

History isolation noteReplicate 1 created this history and completed bcftools stats. Replicate 3 later opened the same history and downloaded replicate 1's output, so replicate 3 is marked invalid.

Validity review: This replicate directly downloaded and used replicate 1's completed bcftools output. It is invalid because the Galaxy analysis was not independently executed.

Execution condition

Open-ended code with skills

Codex GPT-5.5

3 primary replicates
Codex GPT-5.5

replicate 1

fail

Why it missed

Benchmark provenance issueThis run counted transitions and transversions in the supplied raw VCF and obtained 2.56. The benchmark's 2.68 callset cannot be reconstructed from the supplied files.
Answer2.56
Workflow
Local analysisbcftoolsVCFtools
Total tokens
193.7K
Output
3.7K
Run trace
Codex GPT-5.5

replicate 2

fail

Why it missed

Benchmark provenance issueThis run counted transitions and transversions in the supplied raw VCF and obtained 2.56. The benchmark's 2.68 callset cannot be reconstructed from the supplied files.
Answer2.56
Workflow
Local analysisbcftoolsVCFtools
Total tokens
153.5K
Output
3.5K
Run trace
Codex GPT-5.5

replicate 3

fail

Why it missed

Benchmark provenance issueThis run counted transitions and transversions in the supplied raw VCF and obtained 2.56. The benchmark's 2.68 callset cannot be reconstructed from the supplied files.
Answer2.56
Workflow
Local analysisbcftoolsVCFtools
Total tokens
126.0K
Output
3.1K
Run trace

Codex GPT-5.6 Sol

3 primary replicates
Codex GPT-5.6 Sol

replicate 1

fail

Why it missed

Benchmark provenance issueThis run counted transitions and transversions in the supplied raw VCF and obtained 2.56. The accepted 2.68 callset cannot be reconstructed from the supplied files.
Answer2.56
Workflow
Local analysis
Total tokens
342.5K
Output
2.6K
Run trace
Codex GPT-5.6 Sol

replicate 2

fail

Why it missed

Benchmark provenance issueThis run counted transitions and transversions in the supplied raw VCF and obtained 2.56. The accepted 2.68 callset cannot be reconstructed from the supplied files.
Answer2.56
Workflow
Local analysis
Total tokens
231.4K
Output
3.8K
Run trace
Codex GPT-5.6 Sol

replicate 3

fail

Why it missed

Benchmark provenance issueThis run counted transitions and transversions in the supplied raw VCF and obtained 2.56. The accepted 2.68 callset cannot be reconstructed from the supplied files.
Answer2.56
Workflow
Local analysis
Total tokens
198.4K
Output
3.4K
Run trace

Codex GPT-5.6 Luna

3 primary replicates
Codex GPT-5.6 Luna

replicate 1

fail

Why it missed

Benchmark provenance issueThis run counted transitions and transversions in the supplied raw VCF and obtained 2.56. The accepted 2.68 callset cannot be reconstructed from the supplied files.
Answer2.56
Workflow
Local analysis
Total tokens
455.3K
Output
5.7K
Run trace
Codex GPT-5.6 Luna

replicate 2

fail

Why it missed

Benchmark provenance issueThis run counted transitions and transversions in the supplied raw VCF and obtained 2.56. The accepted 2.68 callset cannot be reconstructed from the supplied files.
Answer2.56
Workflow
Local analysis
Total tokens
396.6K
Output
9.3K
Run trace
Codex GPT-5.6 Luna

replicate 3

fail

Why it missed

Benchmark provenance issueThis run counted transitions and transversions in the supplied raw VCF and obtained 2.56. The accepted 2.68 callset cannot be reconstructed from the supplied files.
Answer2.56
Workflow
Local analysis
Total tokens
457.8K
Output
8.1K
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.
Answer2.56
Workflow
Local analysisbcftools
Total tokens
938.2K
Output
10.9K
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.
Answer2.56
Workflow
Local analysisbcftoolsVCFtools
Total tokens
1.16M
Output
17.5K
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.
Answer2.56
Workflow
Local analysisbcftoolsVCFtools
Total tokens
325.4K
Output
6.8K
Run trace

DeepSeek V4 Pro via Claude CodeSuperseded

3 primary replicates
DeepSeek V4 Pro via Claude Code

replicate 1

fail

Why it missed

Benchmark provenance issueThis run used bcftools or pysam to count the supplied raw VCF and obtained 2.56. The disagreement is about the intended callset, not Ts/Tv arithmetic.
Answer2.56
Workflow
Local analysisbcftoolspysam
Total tokens
355.8K
Output
5.4K
Run trace
DeepSeek V4 Pro via Claude Code

replicate 2

fail

Why it missed

Benchmark provenance issueThis run used bcftools or pysam to count the supplied raw VCF and obtained 2.56. The disagreement is about the intended callset, not Ts/Tv arithmetic.
Answer2.56
Workflow
Local analysisbcftoolspysam
Total tokens
617.3K
Output
9.4K
Run trace
DeepSeek V4 Pro via Claude Code

replicate 3

fail

Why it missed

Benchmark provenance issueThis run used bcftools or pysam to count the supplied raw VCF and obtained 2.56. The disagreement is about the intended callset, not Ts/Tv arithmetic.
Answer2.56
Workflow
Local analysisbcftools
Total tokens
517.0K
Output
9.3K
Run trace

bix-61-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 0.26M tokens; previous website Galaxy averaged 0.51M; the new Galaxy runs averaged 0.44M, or 1.70× 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