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CompBioBench item

mystery-peak-set-q1

Question

The file mystery.peak.set.q1.bed.gz contains genomic intervals for six distinct peak sets (S1–S6), all mapped to the hg38 reference genome. Each peak set represents accessible chromatin regions identified under different experimental conditions. One of these peak sets corresponds to a chromatin accessibility pattern that is strongly depleted in large public collections of unperturbed human samples, including both primary tissues and established cell lines. Identify which peak set (S1–S6) shows this depletion and report its name.

Predicted answer
S5Most likely answer for this question; not uniquely determined from submitted scores.
Domain
Epigenomics
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-only
AnswerS5
Workflow
Mystery peak public catalog overlapMystery peak DHS depletion check
Codex GPT-5.5

Replicate 2

Matches predictionUDT + standard tools
AnswerS5
Workflow
DHS depletion analysisDHS depletion analysis v2UDT render probeUDT echo probeGrep2 more tools
Total tokens
1.4M
Output
14.4K
Codex GPT-5.5

Replicate 3

Matches predictionUDT + standard tools
AnswerS5
Workflow
Peak set depletion overlap analysisPeak set depletion overlap analysis v2UDT render probe
Total tokens
6.4M
Output
24.6K

Codex GPT-5.6 Sol

3 replicates
Codex GPT-5.6 Sol

Replicate 1

Matches predictionStandard tools only
AnswerS5
Workflow
Ucsc BigbedtobedBedtools IntersectbedSelect columnsDatamash OpsSort rows2 more tools
Codex GPT-5.6 Sol

Replicate 2

Matches predictionUDT-only
AnswerS5
Workflow
Peak-set diagnostics Q1ENCODE DHS Index peak-set overlap Q1
Total tokens
3.8M
Output
11.8K
Codex GPT-5.6 Sol

Replicate 3

Matches predictionStandard tools only
AnswerS5
Workflow
Count1Ucsc BigbedtobedBedtools IntersectbedShow Tail1Converter Gz To Uncompressed2 more tools
Total tokens
3.8M
Output
10.0K

Codex + DeepSeek-v4-pro-0813

3 replicates
Codex + DeepSeek-v4-pro-0813

Replicate 1

Matches predictionStandard tools only
AnswerS5
Workflow
Bedtools IntersectbedBedtools GroupbybedTp Sort Header Tool
Total tokens
5.0M
Output
31.2K
Codex + DeepSeek-v4-pro-0813

Replicate 2

Matches predictionStandard tools only
AnswerS5
Workflow
Upload1Data FetchUcsc BigbedtobedBedtools IntersectbedCount12 more tools
Total tokens
3.2M
Output
17.5K
Codex + DeepSeek-v4-pro-0813

Replicate 3

Matches predictionStandard tools only
AnswerS5
Workflow
Bedtools IntersectbedBedtools GroupbybedSort rows
Total tokens
2.3M
Output
13.0K

Codex GPT-5.6 Luna

3 replicates
Codex GPT-5.6 Luna

Replicate 1

Matches predictionStandard tools only
AnswerS5
Workflow
Datamash OpsUpload1Bedtools IntersectbedBedtools GroupbybedJoin datasets1 more tools
Total tokens
18.8M
Output
39.0K
Codex GPT-5.6 Luna

Replicate 2

Matches predictionStandard tools only
AnswerS5
Workflow
Count1Bedtools Intersectbed
Total tokens
6.6M
Output
23.7K
Codex GPT-5.6 Luna

Replicate 3

Matches predictionStandard tools only
AnswerS5
Workflow
Wc GnuTp Split On ColumnUpload1Ucsc BigbedtobedBedtools Intersectbed

Anycode

13/13 terminal item results

Codex GPT-5.5

3 replicates
Codex GPT-5.5

Replicate 1

Matches prediction
AnswerS5
Workflow
Local codeBedtoolsPython
Codex GPT-5.5

Replicate 2

Matches prediction
AnswerS5
Workflow
Local codeBedtoolsPython
Codex GPT-5.5

Replicate 3

Matches prediction
AnswerS5
Workflow
Local codeBedtoolsPython

Codex GPT-5.6 Sol

3 replicates
Codex GPT-5.6 Sol

Replicate 1

Matches prediction
AnswerS5
Workflow
Local codeBedtools
Codex GPT-5.6 Sol

Replicate 2

Matches prediction
AnswerS5
Workflow
Local codeBedtools
Codex GPT-5.6 Sol

Replicate 3

Matches prediction
AnswerS5
Workflow
Local codePythonBedtools

Codex + DeepSeek-v4-pro-0813

3 replicates
Codex + DeepSeek-v4-pro-0813

Replicate 1

Matches prediction
AnswerS5
Workflow
Local codeBedtoolsPythonSciPy
Total tokens
725.1K
Output
12.6K
Codex + DeepSeek-v4-pro-0813

Replicate 2

Matches prediction
AnswerS5
Workflow
Local codePythonBedtools
Total tokens
513.7K
Output
8.8K
Codex + DeepSeek-v4-pro-0813

Replicate 3

Matches prediction
AnswerS5
Workflow
Local codePythonBedtools
Total tokens
1.7M
Output
17.5K

Codex GPT-5.6 Luna

3 replicates
Codex GPT-5.6 Luna

Replicate 1

Matches prediction
AnswerS5
Workflow
Local codeBedtoolsSamtoolsPython
Codex GPT-5.6 Luna

Replicate 2

RerunMatches prediction
AnswerS5
Workflow
Open-ended code
Total tokens
1.8M
Output
14.7K
Codex GPT-5.6 Luna

Replicate 3

Matches prediction
AnswerS5
Workflow
Local codeBedtools

Codex GPT-6 Astra

1 replicate
Codex GPT-6 Astra

Replicate 1

Matches prediction
AnswerS5
Workflow
Local codePython
Total tokens
243.9K
Output
3.8K