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CompBioBench item

identify-related-q1

Question

You are given identify.related.q1.tfam and identify.related.q1.tped.gz files of genotypes. I need to know if there are any 1st-degree relatives. Print a comma separated, sorted list of all individuals with a 1st-degree or closer relative in the dataset (e.g. SAMPLE_001,SAMPLE_002). If no such individuals exist, print None.

Predicted answer
SAMPLE_081,SAMPLE_109,SAMPLE_137,SAMPLE_155Most likely answer for this question; not uniquely determined from submitted scores.
Domain
Population Genetics
Question style
Metadata Recovery

An answer can be uniquely inferred for 54 of 100 questions from submitted scores. Green: correct · Red: incorrect. For questions without a uniquely determined answer: Blue: matches prediction · Orange: differs from prediction. These are inferred answer checks, not official per-question grades.

Galaxy

12/12 terminal item results

UDT = user-defined tool: custom code executed by Galaxy. Route badges summarize analysis tools, excluding uploads and automatic conversions. How usage is counted.

Codex GPT-5.5

3 replicates
Codex GPT-5.5

Replicate 1

Matches predictionUDT + standard tools
AnswerSAMPLE_081,SAMPLE_109,SAMPLE_137,SAMPLE_155
Workflow
PLINKUDT render probeUDT render probe v2UDT render probe v3Plink
Galaxy historyAgent trace
Codex GPT-5.5

Replicate 2

Matches predictionUDT + standard tools
AnswerSAMPLE_081,SAMPLE_109,SAMPLE_137,SAMPLE_155
Workflow
TPED TFAM diagnosticTPED TFAM diagnostic v2UDT minimal probe 001Plink
Total tokens
1.9M
Output
13.7K
Galaxy historyAgent trace
Codex GPT-5.5

Replicate 3

RerunMatches predictionUDT-only
AnswerSAMPLE_081,SAMPLE_109,SAMPLE_137,SAMPLE_155
Workflow
TPED TFAM PLINK relatednessTPED TFAM PLINK relatedness scripted
Total tokens
934.9K
Output
8.5K
Galaxy historyAgent trace

Codex GPT-5.6 Sol

3 replicates
Codex GPT-5.6 Sol

Replicate 1

Matches predictionUDT-only
AnswerSAMPLE_081,SAMPLE_109,SAMPLE_137,SAMPLE_155
Workflow
PLINKClassify first-degree relatives from PLINK IBD
Total tokens
1.1M
Output
5.5K
Galaxy historyAgent trace
Codex GPT-5.6 Sol

Replicate 2

Matches predictionUDT-only
AnswerSAMPLE_081,SAMPLE_109,SAMPLE_137,SAMPLE_155
Workflow
PLINK
Total tokens
3.9M
Output
12.7K
Galaxy historyAgent trace
Codex GPT-5.6 Sol

Replicate 3

Matches predictionUDT + standard tools
AnswerSAMPLE_081,SAMPLE_109,SAMPLE_137,SAMPLE_155
Workflow
PLINKTPED structure diagnostic for relatives q1Converter Gz To UncompressedRandom Lines1Select columns8 more tools
Total tokens
39.2M
Output
61.6K
Galaxy historyAgent trace

Codex + DeepSeek-v4-pro-0813

3 replicates
Codex + DeepSeek-v4-pro-0813

Replicate 1

Matches predictionUDT + standard tools
AnswerSAMPLE_081,SAMPLE_109,SAMPLE_137,SAMPLE_155
Workflow
PLINKTp Sed ToolTp Cut ToolFilter TabularExtract related IDs
Total tokens
2.7M
Output
19.4K
Galaxy historyAgent trace
Codex + DeepSeek-v4-pro-0813

Replicate 2

Matches predictionUDT-only
AnswerSAMPLE_081,SAMPLE_109,SAMPLE_137,SAMPLE_155
Workflow
PLINKExtract related individuals from PLINK genome
Total tokens
859.1K
Output
11.5K
Galaxy historyAgent trace
Codex + DeepSeek-v4-pro-0813

Replicate 3

Matches predictionUDT + standard tools
AnswerSAMPLE_081,SAMPLE_109,SAMPLE_137,SAMPLE_155
Workflow
PLINKProbe wcProbe wc v2Plink
Total tokens
6.0M
Output
32.4K
Galaxy historyAgent trace

Codex GPT-5.6 Luna

3 replicates
Codex GPT-5.6 Luna

Replicate 1

Matches predictionUDT + standard tools
AnswerSAMPLE_081,SAMPLE_109,SAMPLE_137,SAMPLE_155
Workflow
PLINKUDT render smoke testUDT render smoke test v2UDT render smoke test v3Converter Gz To Uncompressed12 more tools
Galaxy historyAgent trace
Codex GPT-5.6 Luna

Replicate 2

Matches predictionUDT-only
AnswerSAMPLE_081,SAMPLE_109,SAMPLE_137,SAMPLE_155
Workflow
Converter Gz To UncompressedPLINKRank IBD pairs by PI_HAT
Total tokens
3.4M
Output
15.5K
Galaxy historyAgent trace
Codex GPT-5.6 Luna

Replicate 3

Matches predictionUDT-only
AnswerSAMPLE_081,SAMPLE_109,SAMPLE_137,SAMPLE_155
Workflow
Converter Gz To UncompressedPLINK
Total tokens
1.2M
Output
10.5K
Galaxy historyAgent trace

Anycode

13/13 terminal item results

Codex GPT-5.5

3 replicates
Codex GPT-5.5

Replicate 1

Matches prediction
AnswerSAMPLE_081,SAMPLE_109,SAMPLE_137,SAMPLE_155
Workflow
Local codePLINKPython
Agent trace
Codex GPT-5.5

Replicate 2

Matches prediction
AnswerSAMPLE_081,SAMPLE_109,SAMPLE_137,SAMPLE_155
Workflow
Local codePLINKPython
Agent trace
Codex GPT-5.5

Replicate 3

Matches prediction
AnswerSAMPLE_081,SAMPLE_109,SAMPLE_137,SAMPLE_155
Workflow
Local codePLINKPythonR
Agent trace

Codex GPT-5.6 Sol

3 replicates
Codex GPT-5.6 Sol

Replicate 1

Matches prediction
AnswerSAMPLE_081,SAMPLE_109,SAMPLE_137,SAMPLE_155
Workflow
Local codePLINKPython
Agent trace
Codex GPT-5.6 Sol

Replicate 2

Matches prediction
AnswerSAMPLE_081,SAMPLE_109,SAMPLE_137,SAMPLE_155
Workflow
Local codePLINKPython
Agent trace
Codex GPT-5.6 Sol

Replicate 3

Matches prediction
AnswerSAMPLE_081,SAMPLE_109,SAMPLE_137,SAMPLE_155
Workflow
Local codePLINKPython
Agent trace

Codex + DeepSeek-v4-pro-0813

3 replicates
Codex + DeepSeek-v4-pro-0813

Replicate 1

Matches prediction
AnswerSAMPLE_081,SAMPLE_109,SAMPLE_137,SAMPLE_155
Workflow
Local codePLINKBCFtoolsRPython
Total tokens
810.7K
Output
18.9K
Agent trace
Codex + DeepSeek-v4-pro-0813

Replicate 2

Matches prediction
AnswerSAMPLE_081,SAMPLE_109,SAMPLE_137,SAMPLE_155
Workflow
Local codePLINKSciPyPythonBCFtools1 more tools
Total tokens
383.2K
Output
4.0K
Agent trace
Codex + DeepSeek-v4-pro-0813

Replicate 3

Matches prediction
AnswerSAMPLE_081,SAMPLE_109,SAMPLE_137,SAMPLE_155
Workflow
Local codePLINKBCFtoolsPythonSciPy
Total tokens
230.3K
Output
4.9K
Agent trace

Codex GPT-5.6 Luna

3 replicates
Codex GPT-5.6 Luna

Replicate 1

Matches prediction
AnswerSAMPLE_081,SAMPLE_109,SAMPLE_137,SAMPLE_155
Workflow
Local codePLINKBCFtoolsPython
Agent trace
Codex GPT-5.6 Luna

Replicate 2

Matches prediction
AnswerSAMPLE_081,SAMPLE_109,SAMPLE_137,SAMPLE_155
Workflow
Local codePLINKBCFtoolsRPython
Agent trace
Codex GPT-5.6 Luna

Replicate 3

Matches prediction
AnswerSAMPLE_081,SAMPLE_109,SAMPLE_137,SAMPLE_155
Workflow
Local codePLINKBCFtoolsPythonSciPy1 more tools
Agent trace

Codex GPT-6 Astra

1 replicate
Codex GPT-6 Astra

Replicate 1

Matches prediction
AnswerSAMPLE_081,SAMPLE_109,SAMPLE_137,SAMPLE_155
Workflow
Local codePLINKPythonSciPy
Total tokens
190.4K
Output
1.4K
Agent trace