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CompBioBench item

bigwig-density-q1

Question

From the given ENCFF822FDB.bigWig file corresponding to an ENCODE DNase-seq experiment in mouse brain (mm10), find the 1Mbp interval with the 3rd highest total signal intensity. Consider only those intervals that start at multiples of 1Mbp, and ignore intervals at chromosome ends that are smaller than 1Mbp. Consider only chromosomes 1-19. Report as 0-based coordinates in chr:start-end format (no commas).

Predicted answer
chr8:70000000-71000000Most likely answer for this question; not uniquely determined from submitted scores.
Domain
Epigenomics
Question style
Routine Analysis

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
Answerchr8:70000000-71000000
Workflow
Rank bigWig 1Mb bins and report third
Codex GPT-5.5

Replicate 2

Matches predictionUDT-only
Answerchr8:70000000-71000000
Workflow
bigWig diagnosticbigWig top 1Mb bins
Total tokens
411.5K
Output
3.4K
Codex GPT-5.5

Replicate 3

Matches predictionUDT-only
Answerchr8:70000000-71000000
Workflow
bigWig 1Mb diagnosticRank bigWig 1Mb binsValidate top bigWig bins
Total tokens
424.9K
Output
6.0K

Codex GPT-5.6 Sol

3 replicates
Codex GPT-5.6 Sol

Replicate 1

Matches predictionUDT + standard tools
Answerchr8:70000000-71000000
Workflow
Bedtools MakewindowsbedUDT smoke testUDT smoke bracedRank complete 1 Mb BigWig windowsVerify top BigWig windows independently1 more tools
Codex GPT-5.6 Sol

Replicate 2

Matches predictionUDT + standard tools
Answerchr8:70000000-71000000
Workflow
Inspect BigWig chromosome metadataBedtools MakewindowsbedFilter rowsFilter TabularRank exact BigWig signal in 1 Mb windows
Total tokens
2.1M
Output
9.2K
Codex GPT-5.6 Sol

Replicate 3

Matches predictionUDT-only
Answerchr8:70000000-71000000
Workflow
BigWig 1 Mb window diagnosticRank exact BigWig 1 Mb total-signal windows
Total tokens
2.6M
Output
11.6K

Codex + DeepSeek-v4-pro-0813

3 replicates
Codex + DeepSeek-v4-pro-0813

Replicate 1

Matches predictionUDT + standard tools
Answerchr8:70000000-71000000
Workflow
No Galaxy tool job recorded
Total tokens
9.8M
Output
54.8K
Codex + DeepSeek-v4-pro-0813

Replicate 2

Matches predictionStandard tools only
Answerchr8:70000000-71000000
Workflow
No Galaxy tool job recorded
Total tokens
23.3M
Output
75.8K
Codex + DeepSeek-v4-pro-0813

Replicate 3

Matches predictionStandard tools only
Answerchr8:70000000-71000000
Workflow
BigwigtowigFilter TabularGrepBedtools MakewindowsbedWiggle2Simple13 more tools
Total tokens
10.7M
Output
42.1K

Codex GPT-5.6 Luna

3 replicates
Codex GPT-5.6 Luna

Replicate 1

Matches predictionUDT + standard tools
Answerchr8:70000000-71000000
Workflow
bigWig diagnosticUDT template probeUDT render probeDeeptools Multi Bigwig SummaryFilter Tabular3 more tools
Total tokens
12.1M
Output
49.3K
Codex GPT-5.6 Luna

Replicate 2

Matches predictionUDT + standard tools
Answerchr8:70000000-71000000
Workflow
Deeptools Multi Bigwig SummaryBigWig window statistics probeBedtools MakewindowsbedBigwigtowigWiggle2Simple13 more tools
Total tokens
16.9M
Output
39.8K
Codex GPT-5.6 Luna

Replicate 3

Matches predictionUDT + standard tools
Answerchr8:70000000-71000000
Workflow
Deeptools Multi Bigwig SummaryBigWig Window DiagnosticRank BigWig 1Mbp Windows
Total tokens
2.2M
Output
17.7K

Anycode

13/13 terminal item results

Codex GPT-5.5

3 replicates
Codex GPT-5.5

Replicate 1

Matches prediction
Answerchr8:70000000-71000000
Workflow
Local codePython
Codex GPT-5.5

Replicate 2

Matches prediction
Answerchr8:70000000-71000000
Workflow
Local codePython
Codex GPT-5.5

Replicate 3

Matches prediction
Answerchr8:70000000-71000000
Workflow
Local codePython

Codex GPT-5.6 Sol

3 replicates
Codex GPT-5.6 Sol

Replicate 1

Matches prediction
Answerchr8:70000000-71000000
Workflow
Local codePython
Codex GPT-5.6 Sol

Replicate 2

Matches prediction
Answerchr8:70000000-71000000
Workflow
Local codePython
Codex GPT-5.6 Sol

Replicate 3

Matches prediction
Answerchr8:70000000-71000000
Workflow
Local codePython

Codex + DeepSeek-v4-pro-0813

3 replicates
Codex + DeepSeek-v4-pro-0813

Replicate 1

Matches prediction
Answerchr8:70000000-71000000
Workflow
Local codePython
Total tokens
211.6K
Output
6.3K
Codex + DeepSeek-v4-pro-0813

Replicate 2

Matches prediction
Answerchr8:70000000-71000000
Workflow
Local codePythonSamtoolsBedtools
Total tokens
385.5K
Output
11.7K
Codex + DeepSeek-v4-pro-0813

Replicate 3

Matches prediction
Answerchr8:70000000-71000000
Workflow
Local codePython
Total tokens
316.3K
Output
12.2K

Codex GPT-5.6 Luna

3 replicates
Codex GPT-5.6 Luna

Replicate 1

Matches prediction
Answerchr8:70000000-71000000
Workflow
Local codePythonpysam
Codex GPT-5.6 Luna

Replicate 2

Matches prediction
Answerchr8:70000000-71000000
Workflow
Local codePython
Codex GPT-5.6 Luna

Replicate 3

Matches prediction
Answerchr8:70000000-71000000
Workflow
Local codePython

Codex GPT-6 Astra

1 replicate
Codex GPT-6 Astra

Replicate 1

Matches prediction
Answerchr8:70000000-71000000
Workflow
Local codePython
Total tokens
109.1K
Output
1.2K