Codex GPT-5.5
Replicate 1
CorrectUDT-only
Answer
AACATGGAGCGCCGGG-1Workflow
ATAC doublet diagnosticATAC simulated doublet scoringATAC simulated doublet scoring exclude self pairsATAC AMULET-style overlap doublet scoring
Question
atac.doublet.q1.bed.gz contains a fragment file from a scATAC-seq sample (hg38). Barcodes with low read counts have been filtered out. Look for doublets. Return the coordinates of any one doublet, if any. Respond only with the label of the barcode in the format: "AAATGGAACGTTAAAG-1", or "None".
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 resultsUDT = 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 replicatesCodex GPT-5.5
Replicate 2
CorrectUDT-only
Answer
AACATGGAGCGCCGGG-1Workflow
ATAC fragment diagnosticsATAC overlap doublet scanATAC candidate overlap loci
- Total tokens
- 403.7K
- Output
- 6.7K
Codex GPT-5.5
Replicate 3
CorrectUDT-only
Answer
AACATGGAGCGCCGGG-1Workflow
ATAC doublet fragment diagnosticsATAC doublet locus validation
- Total tokens
- 355.9K
- Output
- 5.9K
Codex GPT-5.6 Sol
3 replicatesCodex GPT-5.6 Sol
Replicate 1
CorrectUDT + standard tools
Answer
AACATGGAGCGCCGGG-1Workflow
Snapatac2 PreprocessingDatamash OpsTp Sort Header ToolExtract scATAC doublet annotationsAnnData1 more tools
Codex GPT-5.6 Sol
Replicate 2
IncorrectUDT + standard tools
Answer
AACTATTGAGACATTT-1Workflow
scATAC fragment diagnosticsSnapatac2 PreprocessingAnndata InspectSort rowsscATAC doublet score consensus5 more tools
- Total tokens
- 12.9M
- Output
- 30.5K
Codex GPT-5.6 Sol
Replicate 3
CorrectUDT + standard tools
Answer
AACATGGAGCGCCGGG-1Workflow
ATAC fragment diagnosticsSciPyATAC doublet LSI consensusSnapatac2 PreprocessingAnnData1 more tools
- Total tokens
- 10.4M
- Output
- 25.9K
Codex + DeepSeek-v4-pro-0813
3 replicatesCodex + DeepSeek-v4-pro-0813
Replicate 1
CorrectUDT + standard tools
Answer
AACATGGAGCGCCGGG-1Workflow
Snapatac2 PreprocessingAnndata InspectTp Sort Header ToolAMULET overlap counter
- Total tokens
- 5.0M
- Output
- 29.2K
Codex + DeepSeek-v4-pro-0813
Replicate 2
RerunCorrectUDT + standard tools
Answer
AACATGGAGCGCCGGG-1Workflow
snapatac2 preprocessing → anndata inspect → User-defined tool
- Total tokens
- 6.3M
- Output
- 35.3K
Codex + DeepSeek-v4-pro-0813
Replicate 3
RerunCorrectUDT + standard tools
Answer
AACATGGAGCGCCGGG-1Workflow
Group overlapping fragmentsSingle-cell preprocessingScrublet explorationAMULET doublet analysis
- Total tokens
- 13.1M
- Output
- 36.7K
Codex GPT-5.6 Luna
3 replicatesCodex GPT-5.6 Luna
Replicate 1
IncorrectUDT + standard tools
Answer
TCGTATGACCGTTTTG-1Workflow
Tp Head ToolSnapatac2 PreprocessingAnndata ExportExtract Scrublet ObservationsInspect H5AD Observation Encoding13 more tools
- Total tokens
- 10.6M
- Output
- 56.7K
Codex GPT-5.6 Luna
Replicate 2
CorrectUDT + standard tools
Answer
AACATGGAGCGCCGGG-1Workflow
Snapatac2 PreprocessingAnndata ExportSciPyAMULET runtime probeAMULET fragment-file doublet detection
- Total tokens
- 13.5M
- Output
- 43.1K
Codex GPT-5.6 Luna
Replicate 3
IncorrectStandard tools only
Answer
GTTGCGGTTCCGCTCG-1Workflow
Snapatac2 PreprocessingAnndata ExportAnndata InspectTp Sort Header Tool
- Total tokens
- 10.0M
- Output
- 33.2K
Anycode
13/13 terminal item resultsCodex GPT-5.5
3 replicatesCodex GPT-5.5
Replicate 1
Correct
Answer
AACATGGAGCGCCGGG-1Workflow
Local codePython
Codex GPT-5.5
Replicate 2
Correct
Answer
AACATGGAGCGCCGGG-1Workflow
Local codeBedtoolsRPythonSciPy2 more tools
Codex GPT-5.5
Replicate 3
Correct
Answer
AACATGGAGCGCCGGG-1Workflow
Local codePythonSciPyAnnDataScanpy
Codex GPT-5.6 Sol
3 replicatesCodex GPT-5.6 Sol
Replicate 1
Correct
Answer
AACATGGAGCGCCGGG-1Workflow
Local codePythonSciPyBedtools
Codex GPT-5.6 Sol
Replicate 2
Correct
Answer
AACATGGAGCGCCGGG-1Workflow
Local codePythonRSciPyBedtools
Codex GPT-5.6 Sol
Replicate 3
Correct
Answer
AACATGGAGCGCCGGG-1Workflow
Local codePythonSciPy
Codex + DeepSeek-v4-pro-0813
3 replicatesCodex + DeepSeek-v4-pro-0813
Replicate 1
Correct
Answer
AACATGGAGCGCCGGG-1Workflow
Local codePythonScanpyAnnDataSciPy3 more tools
- Total tokens
- 2.7M
- Output
- 26.7K
Codex + DeepSeek-v4-pro-0813
Replicate 2
Correct
Answer
AACATGGAGCGCCGGG-1Workflow
Local codePythonSciPyAnnDataScanpy1 more tools
- Total tokens
- 4.7M
- Output
- 30.2K
Codex + DeepSeek-v4-pro-0813
Replicate 3
Incorrect
Answer
GCGACACGCCGGGCAC-1Workflow
Local codePythonSciPyScanpyAnnData1 more tools
- Total tokens
- 28.7M
- Output
- 114.5K
Codex GPT-5.6 Luna
3 replicatesCodex GPT-5.6 Luna
Replicate 1
Correct
Answer
AACATGGAGCGCCGGG-1Workflow
Local codePythonSciPyAnnDataScanpy2 more tools
Codex GPT-5.6 Luna
Replicate 2
Correct
Answer
AACATGGAGCGCCGGG-1Workflow
Local codePythonSciPyAnnDataSamtools3 more tools
Codex GPT-5.6 Luna
Replicate 3
Correct
Answer
AACATGGAGCGCCGGG-1Workflow
Local codePythonSciPyBedtoolsSamtools2 more tools
Codex GPT-6 Astra
1 replicateCodex GPT-6 Astra
Replicate 1
Correct
Answer
AACATGGAGCGCCGGG-1Workflow
Local codePythonSciPyScanpyAnnData
- Total tokens
- 317.9K
- Output
- 5.1K