BixBench current item

bix-61-q2

Question

What is the average coverage depth across the entire reference genome for the MDR sample (SRR35233585) rounded to 4 decimal places? Map the trimmed reads with BWA-MEM (read group @RG\tID:SRR35233585\tSM:SRR35233585\tPL:ILLUMINA\tLB:lib1\tPU:unit1) and use samtools for depth calculations.

Accepted answer
12.1283
Domain
general

Comparison

Pass counts and token totals across the same three replicates.

AgentGalaxy-API codeOpen-ended code
Codex GPT-5.53/3
replicate 1 replicate 2 replicate 3
3.19M total		3/3
replicate 1 replicate 2 replicate 3
1.36M total
Codex GPT-5.6 Sol3/3
replicate 1 replicate 2 replicate 3
4.31M total		3/3
replicate 1 replicate 2 replicate 3
1.16M total
Codex GPT-5.6 Luna3/3
replicate 1 replicate 2 replicate 3
12.18M total		3/3
replicate 1 replicate 2 replicate 3
1.71M total
DeepSeek V4 Pro via Codex3/3
replicate 1 replicate 2 replicate 3
7.05M total		3/3
replicate 1 replicate 2 replicate 3
1.99M total
DeepSeek V4 Pro via Claude Codesuperseded2/3
replicate 1 replicate 2 replicate 3
3.20M total		3/3
replicate 1 replicate 2 replicate 3
3.09M total

Execution condition

Galaxy-API code with skills

Codex GPT-5.5

3 primary replicates
Codex GPT-5.5

replicate 1

pass
Answer12.1283
Workflow
Bwa MemSamtools Depth
Total tokens
948.8K
Output
7.2K
Galaxy historyRun trace
Codex GPT-5.5

replicate 2

pass
Answer12.1283
Workflow
Bwa MemSamtools Depth
Total tokens
982.7K
Output
7.3K
Galaxy historyRun trace
Codex GPT-5.5

replicate 3

pass
Answer12.1283
Workflow
Bwa MemSamtools Depth
Total tokens
1.26M
Output
6.8K
Galaxy historyRun trace

Codex GPT-5.6 Sol

3 primary replicates
Codex GPT-5.6 Sol

replicate 1

pass
Answer12.1283
Workflow
Bwa MemSamtools DepthDatamash summarySummary statisticsBWA-MEM
Total tokens
1.39M
Output
8.6K
Galaxy historyRun trace
Codex GPT-5.6 Sol

replicate 2

pass
Answer12.1283
Workflow
Bwa MemSamtools DepthDatamash summaryBWA-MEM
Total tokens
1.78M
Output
7.8K
Galaxy historyRun trace
Codex GPT-5.6 Sol

replicate 3

pass
Answer12.1283
Workflow
Bwa MemSamtools DepthDatamash summarySummary statisticsBWA-MEM
Total tokens
1.14M
Output
7.7K
Galaxy historyRun trace

Codex GPT-5.6 Luna

3 primary replicates
Codex GPT-5.6 Luna

replicate 1

pass
Answer12.1283
Workflow
Bwa MemSamtools Depth
Total tokens
1.92M
Output
17.2K
Galaxy historyRun trace
Codex GPT-5.6 Luna

replicate 2

pass
Answer12.1283
Workflow
Bwa MemToolshed.G2.Bx.Bwa MemSamtools DepthDatamash summary
Total tokens
4.40M
Output
25.7K
Galaxy historyRun trace
Codex GPT-5.6 Luna

replicate 3

pass
Answer12.1283
Workflow
Bwa MemSamtools DepthDatamash summarySamtools Coverage
Total tokens
5.86M
Output
32.2K
Galaxy historyRun trace

DeepSeek V4 Pro via Codex

3 primary replicates
DeepSeek V4 Pro via Codex

replicate 1

pass
Answer12.1283
Workflow
Bwa MemSamtools DepthDatamash summary
Total tokens
2.36M
Output
19.4K
Galaxy historyRun trace
DeepSeek V4 Pro via Codex

replicate 2

pass
Answer12.1283
Workflow
Bwa MemSamtools DepthDatamash summary
Total tokens
2.75M
Output
14.6K
Galaxy historyRun trace
DeepSeek V4 Pro via Codex

replicate 3

pass
Answer12.1283
Workflow
Bwa MemSamtools Depth
Total tokens
1.94M
Output
14.3K
Galaxy historyRun trace

DeepSeek V4 Pro via Claude CodeSuperseded

3 primary replicates
DeepSeek V4 Pro via Claude Code

replicate 1

fail

Why it missed

Unrequested preprocessingThis run applied Trimmomatic to reads already supplied as trimmed, then mapped the altered reads and obtained 20.5045x coverage. Mapping the supplied reads directly gives about 12.13x.
Answer20.5045
Workflow
TrimmomaticBwa MemSamtools Depth
Total tokens
1.13M
Output
12.9K
Galaxy historyRun trace
DeepSeek V4 Pro via Claude Code

replicate 2

pass
Answer12.1283
Workflow
Bwa Mem
Total tokens
925.1K
Output
9.5K
Galaxy historyRun trace
DeepSeek V4 Pro via Claude Code

replicate 3

pass
Answer12.1283
Workflow
Bwa MemSamtools CoverageSamtools Depth
Total tokens
1.15M
Output
17.6K
Galaxy historyRun trace

Execution condition

Open-ended code with skills

Codex GPT-5.5

3 primary replicates
Codex GPT-5.5

replicate 1

pass
Answer12.1283
Workflow
Local analysisBWA-MEMsamtools depth
Total tokens
317.6K
Output
3.5K
Run trace
Codex GPT-5.5

replicate 2

pass
Answer12.1283
Workflow
Local analysisBWA-MEMsamtools depth
Total tokens
480.6K
Output
5.3K
Run trace
Codex GPT-5.5

replicate 3

pass
Answer12.1283
Workflow
Local analysisBWA-MEMsamtools depth
Total tokens
566.4K
Output
5.5K
Run trace

Codex GPT-5.6 Sol

3 primary replicates
Codex GPT-5.6 Sol

replicate 1

pass
Answer12.1283
Workflow
Local analysis
Total tokens
300.9K
Output
4.0K
Run trace
Codex GPT-5.6 Sol

replicate 2

pass
Answer12.1283
Workflow
Local analysis
Total tokens
300.7K
Output
4.0K
Run trace
Codex GPT-5.6 Sol

replicate 3

pass
Answer12.1283
Workflow
Local analysis
Total tokens
554.8K
Output
5.6K
Run trace

Codex GPT-5.6 Luna

3 primary replicates
Codex GPT-5.6 Luna

replicate 1

pass
Answer12.1283
Workflow
Local analysis
Total tokens
647.7K
Output
10.5K
Run trace
Codex GPT-5.6 Luna

replicate 2

pass
Answer12.1283
Workflow
Local analysis
Total tokens
471.4K
Output
9.6K
Run trace
Codex GPT-5.6 Luna

replicate 3

pass
Answer12.1283
Workflow
Local analysis
Total tokens
591.5K
Output
11.0K
Run trace

DeepSeek V4 Pro via Codex

3 primary replicates
DeepSeek V4 Pro via Codex

replicate 1

pass
Answer12.1283
Workflow
Local analysisBWA-MEMsamtools depthpysam
Total tokens
449.1K
Output
8.8K
Run trace
DeepSeek V4 Pro via Codex

replicate 2

pass
Answer12.1283
Workflow
Local analysisBWA-MEMsamtools depth
Total tokens
1.14M
Output
13.4K
Run trace
DeepSeek V4 Pro via Codex

replicate 3

pass
Answer12.1283
Workflow
Local analysisBWA-MEMsamtools depth
Total tokens
399.8K
Output
7.3K
Run trace

DeepSeek V4 Pro via Claude CodeSuperseded

3 primary replicates
DeepSeek V4 Pro via Claude Code

replicate 1

pass
Answer12.1283
Workflow
Local analysisBWA-MEMsamtools depth
Total tokens
929.9K
Output
6.6K
Run trace
DeepSeek V4 Pro via Claude Code

replicate 2

pass
Answer12.0906
Workflow
Local analysispysamBWA-MEMsamtools depth
Total tokens
1.25M
Output
10.9K
Run trace
DeepSeek V4 Pro via Claude Code

replicate 3

pass
Answer12.0906
Workflow
Local analysispysamBWA-MEMsamtools depth
Total tokens
909.4K
Output
6.1K
Run trace

bix-61-q2 · 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 0.39M tokens; previous website Galaxy averaged 1.44M; the new Galaxy runs averaged 0.58M, or 1.51× 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